Starting phenix.real_space_refine on Thu Feb 5 08:22:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pq3_71782/02_2026/9pq3_71782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pq3_71782/02_2026/9pq3_71782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pq3_71782/02_2026/9pq3_71782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pq3_71782/02_2026/9pq3_71782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pq3_71782/02_2026/9pq3_71782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pq3_71782/02_2026/9pq3_71782.map" } resolution = 3.94 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= 0.008 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 102 5.16 5 C 9750 2.51 5 N 2499 2.21 5 O 3333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 15684 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3558 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3558 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "F" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "I" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3558 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 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: 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: "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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 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: "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: 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: "c" 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 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: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "r" 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: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 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: 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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 Time building chain proxies: 4.39, per 1000 atoms: 0.28 Number of scatterers: 15684 At special positions: 0 Unit cell: (132.825, 133.65, 125.4, 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 102 16.00 O 3333 8.00 N 2499 7.00 C 9750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, 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=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.00 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.08 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 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 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 J 4 " - " MAN J 5 " " MAN Y 4 " - " MAN Y 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA N 3 " - " MAN N 5 " " BMA Y 3 " - " MAN Y 6 " " BMA c 3 " - " MAN c 5 " " BMA n 3 " - " MAN n 6 " " BMA r 3 " - " MAN r 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 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 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG 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-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 135 " " NAG C 602 " - " ASN C 197 " " NAG C 603 " - " ASN C 301 " " NAG D 1 " - " ASN C 88 " " NAG E 1 " - " ASN C 156 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 135 " " NAG G 602 " - " ASN G 197 " " NAG G 603 " - " ASN G 301 " " NAG H 1 " - " ASN C 234 " " NAG I 601 " - " ASN I 135 " " NAG I 602 " - " ASN I 197 " " NAG I 603 " - " ASN I 301 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG L 1 " - " ASN C 289 " " NAG M 1 " - " ASN C 332 " " NAG N 1 " - " ASN C 386 " " NAG O 1 " - " ASN C 442 " " NAG P 1 " - " ASN C 448 " " NAG Q 1 " - " ASN C 160 " " NAG R 1 " - " ASN C 230 " " NAG S 1 " - " ASN C 241 " " NAG T 1 " - " ASN C 339 " " NAG U 1 " - " ASN C 392 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 234 " " NAG Y 1 " - " ASN G 262 " " NAG Z 1 " - " ASN G 276 " " NAG a 1 " - " ASN G 289 " " NAG b 1 " - " ASN G 332 " " NAG c 1 " - " ASN G 386 " " NAG d 1 " - " ASN G 442 " " NAG e 1 " - " ASN G 448 " " NAG f 1 " - " ASN G 160 " " NAG g 1 " - " ASN G 230 " " NAG h 1 " - " ASN G 241 " " NAG i 1 " - " ASN G 339 " " NAG j 1 " - " ASN G 392 " " NAG k 1 " - " ASN I 88 " " NAG l 1 " - " ASN I 156 " " NAG m 1 " - " ASN I 234 " " NAG n 1 " - " ASN I 262 " " NAG o 1 " - " ASN I 276 " " NAG p 1 " - " ASN I 289 " " NAG q 1 " - " ASN I 332 " " NAG r 1 " - " ASN I 386 " " NAG s 1 " - " ASN I 442 " " NAG t 1 " - " ASN I 448 " " NAG u 1 " - " ASN I 160 " " NAG v 1 " - " ASN I 230 " " NAG w 1 " - " ASN I 241 " " NAG x 1 " - " ASN I 339 " " NAG y 1 " - " ASN I 392 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 801.1 milliseconds 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 26.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 544 removed outlier: 4.625A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.728A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.853A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.630A pdb=" N ASN C 392 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 474 through 481 removed outlier: 4.018A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.625A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.728A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 101 through 117 Processing helix chain 'G' and resid 335 through 352 removed outlier: 3.854A pdb=" N GLU G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 388 through 392 removed outlier: 3.631A pdb=" N ASN G 392 " --> pdb=" O GLY G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.904A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU 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: 4.018A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 4.625A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.727A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 101 through 117 Processing helix chain 'I' and resid 335 through 352 removed outlier: 3.853A pdb=" N GLU I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 388 through 392 removed outlier: 3.630A pdb=" N ASN I 392 " --> pdb=" O GLY I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.905A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 429' Processing helix chain 'I' and resid 474 through 481 removed outlier: 4.017A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 5.268A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.550A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.383A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.608A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.440A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 260 through 261 removed outlier: 3.756A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.997A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.306A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.997A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.723A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.561A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.550A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 75 through 76 removed outlier: 7.384A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.608A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.440A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.756A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.997A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS G 331 " --> pdb=" O LEU G 416 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.307A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.997A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE G 468 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.722A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 603 through 609 removed outlier: 5.227A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 76 removed outlier: 7.384A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.608A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.440A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 260 through 261 removed outlier: 3.757A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.997A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS I 331 " --> pdb=" O LEU I 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 271 through 273 removed outlier: 11.307A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.997A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE I 468 " --> pdb=" O THR I 358 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.722A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.78 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: 4455 1.34 - 1.46: 3452 1.46 - 1.58: 7927 1.58 - 1.70: 0 1.70 - 1.81: 138 Bond restraints: 15972 Sorted by residual: bond pdb=" N GLN F 575 " pdb=" CA GLN F 575 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.94e+00 bond pdb=" N GLN B 575 " pdb=" CA GLN B 575 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.78e+00 bond pdb=" N GLN B 577 " pdb=" CA GLN B 577 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.67e+00 bond pdb=" N GLN A 575 " pdb=" CA GLN A 575 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.66e+00 bond pdb=" N GLU B 647 " pdb=" CA GLU B 647 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.57e+00 ... (remaining 15967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 21231 2.50 - 5.00: 377 5.00 - 7.49: 67 7.49 - 9.99: 21 9.99 - 12.49: 3 Bond angle restraints: 21699 Sorted by residual: angle pdb=" C2 NAG t 1 " pdb=" N2 NAG t 1 " pdb=" C7 NAG t 1 " ideal model delta sigma weight residual 124.56 137.05 -12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C2 NAG e 1 " pdb=" N2 NAG e 1 " pdb=" C7 NAG e 1 " ideal model delta sigma weight residual 124.56 137.05 -12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 137.03 -12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" CA GLN B 543 " pdb=" CB GLN B 543 " pdb=" CG GLN B 543 " ideal model delta sigma weight residual 114.10 122.12 -8.02 2.00e+00 2.50e-01 1.61e+01 angle pdb=" CA GLN F 543 " pdb=" CB GLN F 543 " pdb=" CG GLN F 543 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 ... (remaining 21694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 10777 25.51 - 51.01: 641 51.01 - 76.52: 108 76.52 - 102.02: 21 102.02 - 127.53: 3 Dihedral angle restraints: 11550 sinusoidal: 6549 harmonic: 5001 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 168.76 -75.76 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 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 93.00 168.73 -75.73 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 11547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2502 0.071 - 0.142: 357 0.142 - 0.213: 45 0.213 - 0.284: 6 0.284 - 0.355: 6 Chirality restraints: 2916 Sorted by residual: chirality pdb=" CB ILE A 583 " pdb=" CA ILE A 583 " pdb=" CG1 ILE A 583 " pdb=" CG2 ILE A 583 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB ILE B 583 " pdb=" CA ILE B 583 " pdb=" CG1 ILE B 583 " pdb=" CG2 ILE B 583 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE F 583 " pdb=" CA ILE F 583 " pdb=" CG1 ILE F 583 " pdb=" CG2 ILE F 583 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2913 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 519 " 0.016 2.00e-02 2.50e+03 2.22e-02 8.63e+00 pdb=" CG PHE F 519 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE F 519 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE F 519 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 519 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 519 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 519 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 519 " -0.015 2.00e-02 2.50e+03 2.21e-02 8.54e+00 pdb=" CG PHE B 519 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 519 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 519 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 519 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 519 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 519 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 519 " -0.016 2.00e-02 2.50e+03 2.21e-02 8.53e+00 pdb=" CG PHE A 519 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 519 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 519 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 519 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 519 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 519 " 0.000 2.00e-02 2.50e+03 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 7235 2.97 - 3.45: 14821 3.45 - 3.93: 25934 3.93 - 4.42: 27689 4.42 - 4.90: 44981 Nonbonded interactions: 120660 Sorted by model distance: nonbonded pdb=" O5 BMA J 3 " pdb=" O6 BMA J 3 " model vdw 2.486 2.432 nonbonded pdb=" O5 BMA n 3 " pdb=" O6 BMA n 3 " model vdw 2.487 2.432 nonbonded pdb=" O5 BMA Y 3 " pdb=" O6 BMA Y 3 " model vdw 2.487 2.432 nonbonded pdb=" O5 NAG x 1 " pdb=" O6 NAG x 1 " model vdw 2.491 2.432 nonbonded pdb=" O5 NAG i 1 " pdb=" O6 NAG i 1 " model vdw 2.491 2.432 ... (remaining 120655 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'L' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'd' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'p' selection = chain 's' selection = chain 'x' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'X' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'm' selection = chain 'o' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'y' } ncs_group { reference = chain 'J' selection = chain 'Y' selection = chain 'n' } ncs_group { reference = chain 'M' selection = chain 'b' selection = chain 'q' } ncs_group { reference = chain 'N' selection = chain 'c' selection = chain 'r' } 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: 7.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.430 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.051 16158 Z= 0.189 Angle : 0.877 12.488 22224 Z= 0.422 Chirality : 0.053 0.355 2916 Planarity : 0.005 0.064 2532 Dihedral : 14.936 127.528 8211 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.78 % Allowed : 23.44 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1698 helix: -0.19 (0.23), residues: 396 sheet: 0.58 (0.23), residues: 492 loop : -0.71 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 644 TYR 0.013 0.002 TYR B 586 PHE 0.051 0.002 PHE F 519 TRP 0.026 0.002 TRP C 112 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00352 (15972) covalent geometry : angle 0.85825 (21699) SS BOND : bond 0.01093 ( 33) SS BOND : angle 0.81268 ( 66) hydrogen bonds : bond 0.15028 ( 533) hydrogen bonds : angle 6.38876 ( 1545) link_ALPHA1-2 : bond 0.00257 ( 3) link_ALPHA1-2 : angle 1.52620 ( 9) link_ALPHA1-3 : bond 0.00787 ( 9) link_ALPHA1-3 : angle 1.43496 ( 27) link_ALPHA1-6 : bond 0.00572 ( 6) link_ALPHA1-6 : angle 1.32548 ( 18) link_BETA1-4 : bond 0.00733 ( 75) link_BETA1-4 : angle 1.67692 ( 225) link_NAG-ASN : bond 0.00253 ( 60) link_NAG-ASN : angle 1.32619 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 588 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8508 (tm-30) REVERT: C 104 MET cc_start: 0.9223 (tpp) cc_final: 0.8947 (tpp) REVERT: C 434 MET cc_start: 0.7924 (tpp) cc_final: 0.7612 (tpp) REVERT: C 475 MET cc_start: 0.9031 (mmp) cc_final: 0.8795 (mmp) REVERT: C 499 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 574 LYS cc_start: 0.9174 (mttt) cc_final: 0.8955 (pttm) REVERT: B 588 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8603 (tm-30) REVERT: B 590 GLN cc_start: 0.9375 (tp40) cc_final: 0.8914 (tp40) REVERT: G 95 MET cc_start: 0.9252 (ppp) cc_final: 0.8150 (ppp) REVERT: G 104 MET cc_start: 0.9175 (tpp) cc_final: 0.8782 (tpp) REVERT: G 434 MET cc_start: 0.7893 (tpp) cc_final: 0.7580 (tpp) REVERT: G 475 MET cc_start: 0.9026 (mmp) cc_final: 0.8799 (mmp) REVERT: G 499 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8218 (p) REVERT: F 588 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 590 GLN cc_start: 0.9447 (tp40) cc_final: 0.9102 (tp40) REVERT: F 648 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8695 (mm-30) REVERT: I 104 MET cc_start: 0.9192 (tpp) cc_final: 0.8917 (tpt) REVERT: I 434 MET cc_start: 0.7940 (tpp) cc_final: 0.7620 (tpp) REVERT: I 475 MET cc_start: 0.8969 (mmp) cc_final: 0.8608 (mmm) REVERT: I 499 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8239 (p) outliers start: 12 outliers final: 9 residues processed: 112 average time/residue: 0.1153 time to fit residues: 19.9974 Evaluate side-chains 104 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0570 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 195 ASN G 66 HIS I 66 HIS I 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.056234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.041387 restraints weight = 97429.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042589 restraints weight = 59121.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.043357 restraints weight = 44248.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.043800 restraints weight = 37169.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.044122 restraints weight = 33627.480| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16158 Z= 0.127 Angle : 0.604 9.796 22224 Z= 0.280 Chirality : 0.043 0.225 2916 Planarity : 0.004 0.046 2532 Dihedral : 8.286 110.154 4968 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.89 % Allowed : 22.27 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1698 helix: 1.10 (0.26), residues: 402 sheet: 0.85 (0.24), residues: 456 loop : -0.45 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 298 TYR 0.008 0.001 TYR C 318 PHE 0.020 0.001 PHE B 519 TRP 0.031 0.002 TRP C 112 HIS 0.001 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00269 (15972) covalent geometry : angle 0.57169 (21699) SS BOND : bond 0.00185 ( 33) SS BOND : angle 0.39364 ( 66) hydrogen bonds : bond 0.03582 ( 533) hydrogen bonds : angle 4.94040 ( 1545) link_ALPHA1-2 : bond 0.00218 ( 3) link_ALPHA1-2 : angle 1.59082 ( 9) link_ALPHA1-3 : bond 0.00851 ( 9) link_ALPHA1-3 : angle 2.00234 ( 27) link_ALPHA1-6 : bond 0.00468 ( 6) link_ALPHA1-6 : angle 1.48039 ( 18) link_BETA1-4 : bond 0.00476 ( 75) link_BETA1-4 : angle 1.57619 ( 225) link_NAG-ASN : bond 0.00223 ( 60) link_NAG-ASN : angle 1.20976 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 577 GLN cc_start: 0.9108 (pt0) cc_final: 0.8843 (pt0) REVERT: A 588 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 95 MET cc_start: 0.9204 (ppp) cc_final: 0.8741 (ppp) REVERT: C 104 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8960 (tpt) REVERT: B 588 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8561 (tm-30) REVERT: B 590 GLN cc_start: 0.9344 (tp40) cc_final: 0.8921 (tp40) REVERT: G 95 MET cc_start: 0.9197 (ppp) cc_final: 0.7859 (ppp) REVERT: F 577 GLN cc_start: 0.9338 (tt0) cc_final: 0.9135 (tm-30) REVERT: F 588 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8495 (tm-30) REVERT: F 590 GLN cc_start: 0.9413 (tp40) cc_final: 0.8905 (tp40) REVERT: F 629 MET cc_start: 0.9091 (mmm) cc_final: 0.8868 (mmm) REVERT: I 95 MET cc_start: 0.9241 (ppp) cc_final: 0.8787 (ppp) REVERT: I 104 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8952 (tpt) outliers start: 29 outliers final: 13 residues processed: 120 average time/residue: 0.1260 time to fit residues: 22.7042 Evaluate side-chains 97 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN G 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.040188 restraints weight = 99352.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041374 restraints weight = 59961.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.042133 restraints weight = 44919.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.042569 restraints weight = 37888.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.042926 restraints weight = 34339.644| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16158 Z= 0.130 Angle : 0.589 9.558 22224 Z= 0.271 Chirality : 0.043 0.226 2916 Planarity : 0.003 0.040 2532 Dihedral : 7.821 99.403 4959 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.93 % Allowed : 20.64 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1698 helix: 1.60 (0.28), residues: 405 sheet: 0.88 (0.24), residues: 456 loop : -0.34 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 644 TYR 0.008 0.001 TYR C 318 PHE 0.008 0.001 PHE A 519 TRP 0.018 0.001 TRP C 112 HIS 0.002 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00276 (15972) covalent geometry : angle 0.56001 (21699) SS BOND : bond 0.00166 ( 33) SS BOND : angle 0.36737 ( 66) hydrogen bonds : bond 0.03226 ( 533) hydrogen bonds : angle 4.63294 ( 1545) link_ALPHA1-2 : bond 0.00191 ( 3) link_ALPHA1-2 : angle 1.54889 ( 9) link_ALPHA1-3 : bond 0.00861 ( 9) link_ALPHA1-3 : angle 1.98933 ( 27) link_ALPHA1-6 : bond 0.00513 ( 6) link_ALPHA1-6 : angle 1.45729 ( 18) link_BETA1-4 : bond 0.00480 ( 75) link_BETA1-4 : angle 1.49978 ( 225) link_NAG-ASN : bond 0.00201 ( 60) link_NAG-ASN : angle 1.13626 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.580 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: A 530 MET cc_start: 0.8474 (ptp) cc_final: 0.7919 (ttp) REVERT: A 543 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8750 (tm-30) REVERT: A 577 GLN cc_start: 0.9138 (pt0) cc_final: 0.8850 (pt0) REVERT: A 588 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8442 (tm-30) REVERT: C 95 MET cc_start: 0.9206 (ppp) cc_final: 0.8654 (ppp) REVERT: C 104 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8809 (tpt) REVERT: C 499 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 530 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8148 (ttp) REVERT: B 542 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8771 (mmm-85) REVERT: B 588 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 590 GLN cc_start: 0.9351 (tp40) cc_final: 0.8931 (tp40) REVERT: G 95 MET cc_start: 0.9236 (ppp) cc_final: 0.9030 (ppp) REVERT: G 104 MET cc_start: 0.9108 (tpp) cc_final: 0.8729 (tpp) REVERT: G 499 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8323 (p) REVERT: F 543 GLN cc_start: 0.9319 (tm-30) cc_final: 0.8895 (tm-30) REVERT: F 588 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8406 (tm-30) REVERT: F 590 GLN cc_start: 0.9337 (tp40) cc_final: 0.8975 (tp40) REVERT: F 648 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8802 (mm-30) REVERT: I 104 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8843 (tpt) REVERT: I 499 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8361 (p) outliers start: 45 outliers final: 29 residues processed: 131 average time/residue: 0.1122 time to fit residues: 22.4523 Evaluate side-chains 122 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 47 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 85 optimal weight: 0.0670 chunk 141 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.054073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038858 restraints weight = 99124.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.040058 restraints weight = 58532.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040817 restraints weight = 43243.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.041286 restraints weight = 36321.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041511 restraints weight = 32718.459| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16158 Z= 0.202 Angle : 0.661 9.364 22224 Z= 0.306 Chirality : 0.043 0.210 2916 Planarity : 0.003 0.036 2532 Dihedral : 7.743 95.330 4958 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.88 % Allowed : 19.14 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1698 helix: 1.80 (0.28), residues: 405 sheet: 0.89 (0.24), residues: 456 loop : -0.21 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 633 TYR 0.014 0.001 TYR C 435 PHE 0.012 0.001 PHE I 391 TRP 0.015 0.002 TRP G 112 HIS 0.002 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00434 (15972) covalent geometry : angle 0.62983 (21699) SS BOND : bond 0.00259 ( 33) SS BOND : angle 0.64748 ( 66) hydrogen bonds : bond 0.03410 ( 533) hydrogen bonds : angle 4.71837 ( 1545) link_ALPHA1-2 : bond 0.00087 ( 3) link_ALPHA1-2 : angle 1.57278 ( 9) link_ALPHA1-3 : bond 0.00774 ( 9) link_ALPHA1-3 : angle 2.23088 ( 27) link_ALPHA1-6 : bond 0.00473 ( 6) link_ALPHA1-6 : angle 1.52350 ( 18) link_BETA1-4 : bond 0.00468 ( 75) link_BETA1-4 : angle 1.58188 ( 225) link_NAG-ASN : bond 0.00399 ( 60) link_NAG-ASN : angle 1.31020 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 80 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8690 (ptp) cc_final: 0.8408 (ttp) REVERT: A 543 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8715 (tm-30) REVERT: A 588 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8692 (tm-30) REVERT: C 104 MET cc_start: 0.9258 (tpp) cc_final: 0.8998 (tpt) REVERT: C 112 TRP cc_start: 0.9201 (OUTLIER) cc_final: 0.8865 (t60) REVERT: B 530 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8341 (ttp) REVERT: B 588 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8701 (tm-30) REVERT: B 590 GLN cc_start: 0.9523 (tp40) cc_final: 0.8924 (tp40) REVERT: G 95 MET cc_start: 0.9347 (ppp) cc_final: 0.8770 (ppp) REVERT: G 104 MET cc_start: 0.9244 (tpp) cc_final: 0.8886 (tpp) REVERT: G 434 MET cc_start: 0.8184 (tpp) cc_final: 0.7942 (tpp) REVERT: G 499 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8222 (p) REVERT: F 530 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8265 (ttp) REVERT: F 588 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8685 (tm-30) REVERT: F 590 GLN cc_start: 0.9527 (tp40) cc_final: 0.8844 (tp40) REVERT: F 648 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8871 (mm-30) REVERT: I 80 ASN cc_start: 0.9209 (t0) cc_final: 0.8990 (t0) REVERT: I 104 MET cc_start: 0.9301 (tpp) cc_final: 0.9015 (tpt) REVERT: I 112 TRP cc_start: 0.9296 (OUTLIER) cc_final: 0.8966 (t60) outliers start: 75 outliers final: 36 residues processed: 147 average time/residue: 0.1139 time to fit residues: 25.9196 Evaluate side-chains 112 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 71 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 394 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 151 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 149 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.054861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.039542 restraints weight = 98518.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040698 restraints weight = 59755.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.041435 restraints weight = 44948.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.041848 restraints weight = 37935.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.042181 restraints weight = 34549.965| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16158 Z= 0.114 Angle : 0.603 9.414 22224 Z= 0.275 Chirality : 0.043 0.221 2916 Planarity : 0.003 0.037 2532 Dihedral : 7.553 91.183 4956 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.34 % Allowed : 22.53 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1698 helix: 1.61 (0.27), residues: 423 sheet: 1.04 (0.25), residues: 456 loop : -0.16 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 298 TYR 0.007 0.001 TYR B 586 PHE 0.007 0.001 PHE I 53 TRP 0.016 0.001 TRP C 112 HIS 0.003 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00244 (15972) covalent geometry : angle 0.57519 (21699) SS BOND : bond 0.00154 ( 33) SS BOND : angle 0.69776 ( 66) hydrogen bonds : bond 0.03069 ( 533) hydrogen bonds : angle 4.57176 ( 1545) link_ALPHA1-2 : bond 0.00223 ( 3) link_ALPHA1-2 : angle 1.54578 ( 9) link_ALPHA1-3 : bond 0.00897 ( 9) link_ALPHA1-3 : angle 2.07184 ( 27) link_ALPHA1-6 : bond 0.00573 ( 6) link_ALPHA1-6 : angle 1.41390 ( 18) link_BETA1-4 : bond 0.00472 ( 75) link_BETA1-4 : angle 1.44537 ( 225) link_NAG-ASN : bond 0.00180 ( 60) link_NAG-ASN : angle 1.09582 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.396 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: A 530 MET cc_start: 0.8432 (ptp) cc_final: 0.8152 (ttp) REVERT: A 543 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 588 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8506 (tm-30) REVERT: C 104 MET cc_start: 0.9126 (tpp) cc_final: 0.8874 (tpt) REVERT: B 530 MET cc_start: 0.8386 (ptp) cc_final: 0.8151 (ttp) REVERT: B 588 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8565 (tm-30) REVERT: B 590 GLN cc_start: 0.9380 (tp40) cc_final: 0.8803 (tp40) REVERT: G 95 MET cc_start: 0.9274 (ppp) cc_final: 0.7852 (ppp) REVERT: G 104 MET cc_start: 0.9093 (tpp) cc_final: 0.8692 (tpp) REVERT: G 434 MET cc_start: 0.7971 (tpp) cc_final: 0.7709 (tpp) REVERT: G 499 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8356 (p) REVERT: F 530 MET cc_start: 0.8425 (ptp) cc_final: 0.8137 (ttp) REVERT: F 588 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8480 (tm-30) REVERT: F 590 GLN cc_start: 0.9384 (tp40) cc_final: 0.8948 (tp40) REVERT: F 648 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8798 (mm-30) REVERT: I 80 ASN cc_start: 0.9188 (t0) cc_final: 0.8966 (t0) REVERT: I 104 MET cc_start: 0.9175 (tpp) cc_final: 0.8860 (tpt) REVERT: I 302 MET cc_start: 0.8891 (mmm) cc_final: 0.8648 (mmm) outliers start: 36 outliers final: 25 residues processed: 121 average time/residue: 0.1206 time to fit residues: 22.1617 Evaluate side-chains 107 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 444 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 444 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 41 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN G 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.054646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.039398 restraints weight = 99596.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040536 restraints weight = 61614.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.041244 restraints weight = 46706.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.041644 restraints weight = 39716.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041963 restraints weight = 36227.531| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16158 Z= 0.139 Angle : 0.612 9.443 22224 Z= 0.280 Chirality : 0.043 0.219 2916 Planarity : 0.003 0.036 2532 Dihedral : 7.367 84.258 4956 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.52 % Allowed : 21.74 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1698 helix: 1.70 (0.28), residues: 420 sheet: 0.91 (0.24), residues: 468 loop : -0.14 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 298 TYR 0.013 0.001 TYR B 586 PHE 0.025 0.001 PHE B 519 TRP 0.016 0.001 TRP I 112 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00296 (15972) covalent geometry : angle 0.58255 (21699) SS BOND : bond 0.00182 ( 33) SS BOND : angle 0.54476 ( 66) hydrogen bonds : bond 0.03098 ( 533) hydrogen bonds : angle 4.53966 ( 1545) link_ALPHA1-2 : bond 0.00185 ( 3) link_ALPHA1-2 : angle 1.54425 ( 9) link_ALPHA1-3 : bond 0.00882 ( 9) link_ALPHA1-3 : angle 2.22616 ( 27) link_ALPHA1-6 : bond 0.00545 ( 6) link_ALPHA1-6 : angle 1.44047 ( 18) link_BETA1-4 : bond 0.00465 ( 75) link_BETA1-4 : angle 1.49987 ( 225) link_NAG-ASN : bond 0.00229 ( 60) link_NAG-ASN : angle 1.15760 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8558 (ptp) cc_final: 0.8268 (ttp) REVERT: A 543 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 588 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8611 (tm-30) REVERT: C 104 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8942 (tpt) REVERT: B 588 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8658 (tm-30) REVERT: B 590 GLN cc_start: 0.9451 (tp40) cc_final: 0.8705 (tp40) REVERT: G 95 MET cc_start: 0.9276 (ppp) cc_final: 0.8994 (ppp) REVERT: G 104 MET cc_start: 0.9153 (tpp) cc_final: 0.8768 (tpp) REVERT: G 499 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8336 (p) REVERT: F 530 MET cc_start: 0.8538 (ptp) cc_final: 0.8196 (ttp) REVERT: F 588 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8578 (tm-30) REVERT: F 590 GLN cc_start: 0.9436 (tp40) cc_final: 0.8764 (tp40) REVERT: F 648 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8803 (mm-30) REVERT: I 80 ASN cc_start: 0.9214 (t0) cc_final: 0.8961 (t0) REVERT: I 104 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8906 (tpt) REVERT: I 112 TRP cc_start: 0.8982 (OUTLIER) cc_final: 0.8771 (t60) REVERT: I 434 MET cc_start: 0.8976 (tpt) cc_final: 0.8664 (tpt) outliers start: 54 outliers final: 36 residues processed: 135 average time/residue: 0.1061 time to fit residues: 22.5767 Evaluate side-chains 120 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 444 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 145 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 0.0050 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 82 GLN C 343 HIS G 80 ASN I 343 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.039005 restraints weight = 98665.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.040210 restraints weight = 58287.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.040962 restraints weight = 43234.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.041433 restraints weight = 36304.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.041715 restraints weight = 32746.039| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16158 Z= 0.161 Angle : 0.640 9.393 22224 Z= 0.292 Chirality : 0.043 0.216 2916 Planarity : 0.003 0.035 2532 Dihedral : 7.169 70.468 4956 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.52 % Allowed : 22.20 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1698 helix: 1.84 (0.28), residues: 411 sheet: 1.26 (0.25), residues: 429 loop : -0.15 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 298 TYR 0.030 0.001 TYR B 586 PHE 0.033 0.001 PHE A 519 TRP 0.018 0.001 TRP I 112 HIS 0.001 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00345 (15972) covalent geometry : angle 0.61152 (21699) SS BOND : bond 0.00219 ( 33) SS BOND : angle 0.53867 ( 66) hydrogen bonds : bond 0.03118 ( 533) hydrogen bonds : angle 4.52514 ( 1545) link_ALPHA1-2 : bond 0.00164 ( 3) link_ALPHA1-2 : angle 1.55048 ( 9) link_ALPHA1-3 : bond 0.00921 ( 9) link_ALPHA1-3 : angle 2.33797 ( 27) link_ALPHA1-6 : bond 0.00518 ( 6) link_ALPHA1-6 : angle 1.45457 ( 18) link_BETA1-4 : bond 0.00454 ( 75) link_BETA1-4 : angle 1.50391 ( 225) link_NAG-ASN : bond 0.00272 ( 60) link_NAG-ASN : angle 1.19383 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 84 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8666 (ptp) cc_final: 0.8363 (ttp) REVERT: A 543 GLN cc_start: 0.9283 (tm-30) cc_final: 0.8759 (tm-30) REVERT: A 588 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8744 (tm-30) REVERT: C 104 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.9015 (tpt) REVERT: C 112 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.8784 (t60) REVERT: C 201 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9210 (tp) REVERT: B 588 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8789 (tm-30) REVERT: B 590 GLN cc_start: 0.9555 (tp40) cc_final: 0.9271 (tp40) REVERT: G 95 MET cc_start: 0.9305 (ppp) cc_final: 0.8997 (ppp) REVERT: G 104 MET cc_start: 0.9274 (tpp) cc_final: 0.8884 (tpp) REVERT: G 112 TRP cc_start: 0.9150 (OUTLIER) cc_final: 0.8856 (t60) REVERT: G 434 MET cc_start: 0.8108 (tpp) cc_final: 0.7888 (tpp) REVERT: F 530 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8311 (ttp) REVERT: F 588 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8704 (tm-30) REVERT: F 590 GLN cc_start: 0.9523 (tp40) cc_final: 0.8787 (tp40) REVERT: I 80 ASN cc_start: 0.9276 (t0) cc_final: 0.8971 (t0) REVERT: I 104 MET cc_start: 0.9298 (tpp) cc_final: 0.9006 (tpt) outliers start: 54 outliers final: 40 residues processed: 130 average time/residue: 0.1087 time to fit residues: 22.0133 Evaluate side-chains 124 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 112 TRP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 444 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 444 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 58 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 0.0980 chunk 27 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.054596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039223 restraints weight = 100101.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.040407 restraints weight = 61153.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.041100 restraints weight = 46127.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.041579 restraints weight = 39285.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.041797 restraints weight = 35543.831| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16158 Z= 0.116 Angle : 0.628 9.456 22224 Z= 0.288 Chirality : 0.043 0.223 2916 Planarity : 0.003 0.036 2532 Dihedral : 6.809 55.740 4956 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.80 % Allowed : 23.18 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.21), residues: 1698 helix: 2.02 (0.28), residues: 393 sheet: 0.97 (0.24), residues: 474 loop : 0.05 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.018 0.001 TYR B 586 PHE 0.008 0.001 PHE G 53 TRP 0.015 0.001 TRP I 112 HIS 0.003 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00247 (15972) covalent geometry : angle 0.60307 (21699) SS BOND : bond 0.00165 ( 33) SS BOND : angle 0.47957 ( 66) hydrogen bonds : bond 0.03024 ( 533) hydrogen bonds : angle 4.47506 ( 1545) link_ALPHA1-2 : bond 0.00228 ( 3) link_ALPHA1-2 : angle 1.52833 ( 9) link_ALPHA1-3 : bond 0.01043 ( 9) link_ALPHA1-3 : angle 2.08910 ( 27) link_ALPHA1-6 : bond 0.00563 ( 6) link_ALPHA1-6 : angle 1.42702 ( 18) link_BETA1-4 : bond 0.00466 ( 75) link_BETA1-4 : angle 1.44803 ( 225) link_NAG-ASN : bond 0.00171 ( 60) link_NAG-ASN : angle 1.09280 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8594 (ptp) cc_final: 0.8302 (ttp) REVERT: A 543 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8773 (tm-30) REVERT: A 577 GLN cc_start: 0.9176 (pt0) cc_final: 0.8929 (pp30) REVERT: A 588 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 647 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 104 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8889 (tpt) REVERT: C 112 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.8692 (t60) REVERT: C 201 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9209 (tp) REVERT: B 543 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8948 (tm-30) REVERT: B 588 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8661 (tm-30) REVERT: B 590 GLN cc_start: 0.9457 (tp40) cc_final: 0.9058 (tp40) REVERT: G 95 MET cc_start: 0.9286 (ppp) cc_final: 0.7869 (ppp) REVERT: G 104 MET cc_start: 0.9159 (tpp) cc_final: 0.8756 (tpp) REVERT: G 434 MET cc_start: 0.8000 (tpp) cc_final: 0.7789 (tpp) REVERT: F 530 MET cc_start: 0.8556 (ptp) cc_final: 0.8212 (ttp) REVERT: F 588 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8578 (tm-30) REVERT: F 590 GLN cc_start: 0.9414 (tp40) cc_final: 0.8715 (tp40) REVERT: I 80 ASN cc_start: 0.9240 (t0) cc_final: 0.8936 (t0) REVERT: I 95 MET cc_start: 0.9287 (ppp) cc_final: 0.7896 (ppp) REVERT: I 104 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8904 (tpt) REVERT: I 112 TRP cc_start: 0.8900 (OUTLIER) cc_final: 0.8662 (t60) outliers start: 43 outliers final: 29 residues processed: 122 average time/residue: 0.1018 time to fit residues: 19.3042 Evaluate side-chains 118 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 444 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 444 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN G 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.054696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.039522 restraints weight = 98412.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040655 restraints weight = 60644.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041338 restraints weight = 45846.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.041801 restraints weight = 39075.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.042059 restraints weight = 35349.686| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16158 Z= 0.112 Angle : 0.625 11.218 22224 Z= 0.290 Chirality : 0.043 0.224 2916 Planarity : 0.003 0.037 2532 Dihedral : 6.515 55.784 4956 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.67 % Allowed : 23.18 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.12 (0.21), residues: 1698 helix: 1.88 (0.28), residues: 393 sheet: 1.19 (0.25), residues: 438 loop : 0.03 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.020 0.001 TYR B 586 PHE 0.029 0.001 PHE A 519 TRP 0.016 0.001 TRP I 112 HIS 0.003 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00239 (15972) covalent geometry : angle 0.60201 (21699) SS BOND : bond 0.00151 ( 33) SS BOND : angle 0.44060 ( 66) hydrogen bonds : bond 0.03014 ( 533) hydrogen bonds : angle 4.49916 ( 1545) link_ALPHA1-2 : bond 0.00252 ( 3) link_ALPHA1-2 : angle 1.52776 ( 9) link_ALPHA1-3 : bond 0.00939 ( 9) link_ALPHA1-3 : angle 1.63211 ( 27) link_ALPHA1-6 : bond 0.00547 ( 6) link_ALPHA1-6 : angle 1.44147 ( 18) link_BETA1-4 : bond 0.00472 ( 75) link_BETA1-4 : angle 1.45445 ( 225) link_NAG-ASN : bond 0.00160 ( 60) link_NAG-ASN : angle 1.08067 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8576 (ptp) cc_final: 0.8286 (ttp) REVERT: A 543 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8781 (tm-30) REVERT: A 588 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8598 (tm-30) REVERT: A 647 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 104 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8866 (tpt) REVERT: C 112 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.8649 (t60) REVERT: B 588 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8650 (tm-30) REVERT: B 590 GLN cc_start: 0.9478 (tp40) cc_final: 0.9028 (tp40) REVERT: G 104 MET cc_start: 0.9152 (tpp) cc_final: 0.8751 (tpp) REVERT: G 434 MET cc_start: 0.7962 (tpp) cc_final: 0.7740 (tpp) REVERT: F 530 MET cc_start: 0.8548 (ptp) cc_final: 0.8209 (ttp) REVERT: F 588 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8582 (tm-30) REVERT: F 590 GLN cc_start: 0.9431 (tp40) cc_final: 0.8956 (tp40) REVERT: I 80 ASN cc_start: 0.9197 (t0) cc_final: 0.8895 (t0) REVERT: I 95 MET cc_start: 0.9275 (ppp) cc_final: 0.7905 (ppp) REVERT: I 104 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8879 (tpt) outliers start: 41 outliers final: 34 residues processed: 123 average time/residue: 0.1084 time to fit residues: 20.7358 Evaluate side-chains 121 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 444 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 95 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.038589 restraints weight = 99799.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.039664 restraints weight = 61228.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040410 restraints weight = 46944.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.040840 restraints weight = 39513.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.041150 restraints weight = 35840.342| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16158 Z= 0.175 Angle : 0.662 10.221 22224 Z= 0.309 Chirality : 0.043 0.215 2916 Planarity : 0.003 0.035 2532 Dihedral : 6.484 56.107 4956 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.60 % Allowed : 23.05 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1698 helix: 1.62 (0.28), residues: 411 sheet: 1.24 (0.25), residues: 429 loop : -0.07 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 298 TYR 0.011 0.001 TYR B 586 PHE 0.009 0.001 PHE C 391 TRP 0.049 0.002 TRP I 112 HIS 0.002 0.001 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00376 (15972) covalent geometry : angle 0.63653 (21699) SS BOND : bond 0.00235 ( 33) SS BOND : angle 0.47533 ( 66) hydrogen bonds : bond 0.03130 ( 533) hydrogen bonds : angle 4.55113 ( 1545) link_ALPHA1-2 : bond 0.00114 ( 3) link_ALPHA1-2 : angle 1.53917 ( 9) link_ALPHA1-3 : bond 0.00859 ( 9) link_ALPHA1-3 : angle 1.88308 ( 27) link_ALPHA1-6 : bond 0.00514 ( 6) link_ALPHA1-6 : angle 1.48267 ( 18) link_BETA1-4 : bond 0.00458 ( 75) link_BETA1-4 : angle 1.51892 ( 225) link_NAG-ASN : bond 0.00286 ( 60) link_NAG-ASN : angle 1.20962 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8482 (ptp) cc_final: 0.8170 (ttp) REVERT: A 543 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8796 (tm-30) REVERT: A 588 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 647 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7772 (tm-30) REVERT: C 104 MET cc_start: 0.9065 (tpp) cc_final: 0.8787 (tpt) REVERT: B 588 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8579 (tm-30) REVERT: B 590 GLN cc_start: 0.9414 (tp40) cc_final: 0.9018 (tp40) REVERT: G 95 MET cc_start: 0.9266 (ppp) cc_final: 0.8966 (ppp) REVERT: G 104 MET cc_start: 0.9101 (tpp) cc_final: 0.8709 (tpp) REVERT: G 434 MET cc_start: 0.7989 (tpp) cc_final: 0.7771 (tpp) REVERT: F 530 MET cc_start: 0.8494 (ptp) cc_final: 0.8143 (ttp) REVERT: F 588 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8607 (tm-30) REVERT: F 590 GLN cc_start: 0.9363 (tp40) cc_final: 0.8686 (tp40) REVERT: I 80 ASN cc_start: 0.9194 (t0) cc_final: 0.8897 (t0) REVERT: I 95 MET cc_start: 0.9288 (ppp) cc_final: 0.7949 (ppp) REVERT: I 104 MET cc_start: 0.9160 (tpp) cc_final: 0.8847 (tpt) outliers start: 40 outliers final: 36 residues processed: 120 average time/residue: 0.0998 time to fit residues: 18.8992 Evaluate side-chains 119 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 444 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 152 optimal weight: 9.9990 chunk 81 optimal weight: 0.1980 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 105 HIS G 80 ASN G 343 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.053626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038419 restraints weight = 98736.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.039551 restraints weight = 60215.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.040253 restraints weight = 45359.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040689 restraints weight = 38483.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.040944 restraints weight = 34847.239| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16158 Z= 0.184 Angle : 0.674 10.141 22224 Z= 0.317 Chirality : 0.044 0.212 2916 Planarity : 0.003 0.035 2532 Dihedral : 6.581 56.101 4956 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 22.98 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1698 helix: 1.60 (0.28), residues: 414 sheet: 0.95 (0.24), residues: 465 loop : -0.09 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 432 TYR 0.012 0.001 TYR B 586 PHE 0.022 0.001 PHE F 519 TRP 0.053 0.002 TRP I 112 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00397 (15972) covalent geometry : angle 0.64881 (21699) SS BOND : bond 0.00252 ( 33) SS BOND : angle 0.54831 ( 66) hydrogen bonds : bond 0.03279 ( 533) hydrogen bonds : angle 4.66749 ( 1545) link_ALPHA1-2 : bond 0.00167 ( 3) link_ALPHA1-2 : angle 1.57172 ( 9) link_ALPHA1-3 : bond 0.00809 ( 9) link_ALPHA1-3 : angle 1.62050 ( 27) link_ALPHA1-6 : bond 0.00519 ( 6) link_ALPHA1-6 : angle 1.48612 ( 18) link_BETA1-4 : bond 0.00449 ( 75) link_BETA1-4 : angle 1.51477 ( 225) link_NAG-ASN : bond 0.00316 ( 60) link_NAG-ASN : angle 1.26112 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.59 seconds wall clock time: 38 minutes 21.90 seconds (2301.90 seconds total)