Starting phenix.real_space_refine on Thu Mar 5 08:04:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p65_20260/03_2026/6p65_20260.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p65_20260/03_2026/6p65_20260.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6p65_20260/03_2026/6p65_20260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p65_20260/03_2026/6p65_20260.map" model { file = "/net/cci-nas-00/data/ceres_data/6p65_20260/03_2026/6p65_20260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p65_20260/03_2026/6p65_20260.cif" } 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= 0.010 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 129 5.16 5 C 12705 2.51 5 N 3291 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20319 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "E" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "F" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: 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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.97, per 1000 atoms: 0.24 Number of scatterers: 20319 At special positions: 0 Unit cell: (132.25, 136.85, 148.35, 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 129 16.00 O 4194 8.00 N 3291 7.00 C 12705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.13 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.13 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.13 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA Q 3 " - " MAN Q 5 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 5 " " BMA n 3 " - " MAN n 5 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " BETA1-6 " NAG 1 1 " - " FUC 1 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 3 " " NAG m 1 " - " FUC m 3 " NAG-ASN " NAG 0 1 " - " ASN E 392 " " NAG 1 1 " - " ASN E 625 " " NAG A 710 " - " ASN A 187 " " NAG A 729 " - " ASN A 301 " " NAG A 738 " - " ASN A 398 " " NAG A 739 " - " ASN A 442 " " NAG A 740 " - " ASN A 448 " " NAG A 741 " - " ASN A 611 " " NAG A 745 " - " ASN A 637 " " NAG B 710 " - " ASN B 187 " " NAG B 729 " - " ASN B 301 " " NAG B 738 " - " ASN B 398 " " NAG B 739 " - " ASN B 442 " " NAG B 740 " - " ASN B 448 " " NAG B 741 " - " ASN B 611 " " NAG B 745 " - " ASN B 637 " " NAG E 710 " - " ASN E 187 " " NAG E 729 " - " ASN E 301 " " NAG E 738 " - " ASN E 398 " " NAG E 739 " - " ASN E 442 " " NAG E 740 " - " ASN E 448 " " NAG E 741 " - " ASN E 611 " " NAG E 745 " - " ASN E 637 " " NAG I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 230 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 289 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 359 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 625 " " NAG Y 1 " - " ASN B 88 " " NAG Z 1 " - " ASN B 156 " " NAG a 1 " - " ASN B 160 " " NAG b 1 " - " ASN B 197 " " NAG c 1 " - " ASN B 230 " " NAG d 1 " - " ASN B 234 " " NAG e 1 " - " ASN B 241 " " NAG f 1 " - " ASN B 262 " " NAG g 1 " - " ASN B 276 " " NAG h 1 " - " ASN B 289 " " NAG i 1 " - " ASN B 332 " " NAG j 1 " - " ASN B 359 " " NAG k 1 " - " ASN B 386 " " NAG l 1 " - " ASN B 392 " " NAG m 1 " - " ASN B 625 " " NAG n 1 " - " ASN E 88 " " NAG o 1 " - " ASN E 156 " " NAG p 1 " - " ASN E 160 " " NAG q 1 " - " ASN E 197 " " NAG r 1 " - " ASN E 230 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 241 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 276 " " NAG w 1 " - " ASN E 289 " " NAG x 1 " - " ASN E 332 " " NAG y 1 " - " ASN E 359 " " NAG z 1 " - " ASN E 386 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 970.7 milliseconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 20.8% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.655A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.867A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 568 through 568 No H-bonds generated for 'chain 'A' and resid 568 through 568' Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.654A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.868A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 568 through 568 No H-bonds generated for 'chain 'B' and resid 568 through 568' Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.654A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 541 removed outlier: 3.867A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL E 539 " --> pdb=" O ILE E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 548 Processing helix chain 'E' and resid 568 through 568 No H-bonds generated for 'chain 'E' and resid 568 through 568' Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS E 658 " --> pdb=" O GLU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 663 No H-bonds generated for 'chain 'E' and resid 661 through 663' Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.151A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.572A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.651A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 468 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.420A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA H 96 " --> pdb=" O PHE H 100J" (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE H 100J" --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR H 98 " --> pdb=" O LYS H 100H" (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS H 100H" --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY L 91 " --> pdb=" O LEU H 100G" (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS H 100I" --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N LEU L 89 " --> pdb=" O HIS H 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN H 101 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR L 87 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP H 103 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR L 85 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 14 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.151A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.572A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.651A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.895A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE B 468 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 312 removed outlier: 6.420A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.616A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS C 92 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 102 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG C 94 " --> pdb=" O PHE C 100J" (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE C 100J" --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 96 " --> pdb=" O LYS C 100H" (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY D 91 " --> pdb=" O LEU C 100G" (cutoff:3.500A) removed outlier: 9.228A pdb=" N HIS C 100I" --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N LEU D 89 " --> pdb=" O HIS C 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN C 101 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR D 87 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP C 103 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR D 85 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 14 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.150A pdb=" N VAL E 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL E 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR E 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS E 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.571A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.650A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.895A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE E 468 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN E 359 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 303 through 312 removed outlier: 6.421A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'F' and resid 56 through 58 removed outlier: 6.615A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS F 92 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU F 102 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG F 94 " --> pdb=" O PHE F 100J" (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE F 100J" --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA F 96 " --> pdb=" O LYS F 100H" (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY G 91 " --> pdb=" O LEU F 100G" (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS F 100I" --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N LEU G 89 " --> pdb=" O HIS F 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN F 101 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR G 87 " --> pdb=" O ASN F 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP F 103 " --> pdb=" O THR G 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR G 85 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 14 Processing sheet with id=AE3, first strand: chain 'G' and resid 4 through 7 791 hydrogen bonds defined for protein. 2112 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4117 1.32 - 1.44: 5694 1.44 - 1.57: 10692 1.57 - 1.70: 32 1.70 - 1.83: 168 Bond restraints: 20703 Sorted by residual: bond pdb=" CB PHE B 159 " pdb=" CG PHE B 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.57e+01 bond pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.53e+01 bond pdb=" CB PHE A 159 " pdb=" CG PHE A 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.53e+01 bond pdb=" CB TYR D 49 " pdb=" CG TYR D 49 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB TYR G 49 " pdb=" CG TYR G 49 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.74e+01 ... (remaining 20698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 22437 2.08 - 4.16: 4485 4.16 - 6.23: 972 6.23 - 8.31: 164 8.31 - 10.39: 46 Bond angle restraints: 28104 Sorted by residual: angle pdb=" C LYS A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.74 -8.18 1.02e+00 9.61e-01 6.43e+01 angle pdb=" C LYS E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C LYS B 492 " pdb=" N PRO B 493 " pdb=" CA PRO B 493 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.02e+00 9.61e-01 6.33e+01 angle pdb=" CA PHE L 98 " pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 113.80 121.74 -7.94 1.00e+00 1.00e+00 6.31e+01 angle pdb=" CA PHE G 98 " pdb=" CB PHE G 98 " pdb=" CG PHE G 98 " ideal model delta sigma weight residual 113.80 121.74 -7.94 1.00e+00 1.00e+00 6.30e+01 ... (remaining 28099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 13475 21.72 - 43.45: 435 43.45 - 65.17: 82 65.17 - 86.89: 75 86.89 - 108.61: 36 Dihedral angle restraints: 14103 sinusoidal: 7281 harmonic: 6822 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.42 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.41 45.41 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.41 45.41 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 14100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2669 0.114 - 0.227: 784 0.227 - 0.341: 93 0.341 - 0.455: 9 0.455 - 0.569: 9 Chirality restraints: 3564 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.07e+01 chirality pdb=" C1 NAG x 2 " pdb=" O4 NAG x 1 " pdb=" C2 NAG x 2 " pdb=" O5 NAG x 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.87e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.78e+01 ... (remaining 3561 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.098 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG i 1 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.072 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.132 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.098 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG T 1 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.132 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG x 1 " 0.098 2.00e-02 2.50e+03 8.10e-02 8.20e+01 pdb=" C7 NAG x 1 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG x 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG x 1 " -0.132 2.00e-02 2.50e+03 pdb=" O7 NAG x 1 " -0.017 2.00e-02 2.50e+03 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6824 2.84 - 3.35: 17991 3.35 - 3.87: 34923 3.87 - 4.38: 39887 4.38 - 4.90: 64499 Nonbonded interactions: 164124 Sorted by model distance: nonbonded pdb=" N ASN E 398 " pdb=" OD1 ASN E 398 " model vdw 2.319 3.120 nonbonded pdb=" N ASN A 398 " pdb=" OD1 ASN A 398 " model vdw 2.319 3.120 nonbonded pdb=" N ASN B 398 " pdb=" OD1 ASN B 398 " model vdw 2.320 3.120 nonbonded pdb=" O4 NAG Z 2 " pdb=" O6 NAG Z 2 " model vdw 2.339 3.040 nonbonded pdb=" O4 NAG o 2 " pdb=" O6 NAG o 2 " model vdw 2.339 3.040 ... (remaining 164119 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 '0' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain '1' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'Q' selection = chain 'Y' selection = chain 'f' selection = chain 'n' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.590 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.021 0.137 20877 Z= 1.134 Angle : 1.873 10.392 28587 Z= 1.165 Chirality : 0.104 0.569 3564 Planarity : 0.010 0.081 3372 Dihedral : 13.671 108.612 9612 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.44 % Allowed : 0.74 % Favored : 98.82 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.03 % 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: 0.08 (0.16), residues: 2325 helix: -0.98 (0.21), residues: 426 sheet: 0.69 (0.21), residues: 540 loop : 0.27 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 344 TYR 0.059 0.008 TYR D 87 PHE 0.045 0.007 PHE D 98 TRP 0.056 0.010 TRP E 35 HIS 0.015 0.003 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.02113 (20703) covalent geometry : angle 1.85433 (28104) SS BOND : bond 0.02998 ( 39) SS BOND : angle 2.08999 ( 78) hydrogen bonds : bond 0.16470 ( 776) hydrogen bonds : angle 8.85667 ( 2112) link_ALPHA1-3 : bond 0.03712 ( 6) link_ALPHA1-3 : angle 3.39575 ( 18) link_ALPHA1-6 : bond 0.03152 ( 6) link_ALPHA1-6 : angle 3.35491 ( 18) link_BETA1-4 : bond 0.03509 ( 54) link_BETA1-4 : angle 3.26011 ( 162) link_BETA1-6 : bond 0.00215 ( 3) link_BETA1-6 : angle 2.88950 ( 9) link_NAG-ASN : bond 0.02670 ( 66) link_NAG-ASN : angle 2.37063 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 517 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8162 (ttp) cc_final: 0.7957 (ttm) REVERT: A 207 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8129 (tptp) REVERT: A 387 THR cc_start: 0.8811 (p) cc_final: 0.8465 (t) REVERT: A 426 MET cc_start: 0.8776 (tpp) cc_final: 0.8452 (mmm) REVERT: A 536 THR cc_start: 0.8903 (m) cc_final: 0.8684 (p) REVERT: A 571 TRP cc_start: 0.7758 (m100) cc_final: 0.7360 (m100) REVERT: H 11 LEU cc_start: 0.6083 (tt) cc_final: 0.5835 (mp) REVERT: H 33 ASP cc_start: 0.8137 (m-30) cc_final: 0.7845 (t0) REVERT: H 108 LEU cc_start: 0.6739 (tp) cc_final: 0.6387 (tt) REVERT: L 74 THR cc_start: 0.8623 (m) cc_final: 0.8388 (p) REVERT: B 84 MET cc_start: 0.8164 (ttp) cc_final: 0.7930 (ttm) REVERT: B 207 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8323 (tmtt) REVERT: B 358 ILE cc_start: 0.9043 (mt) cc_final: 0.8753 (mm) REVERT: B 387 THR cc_start: 0.8757 (p) cc_final: 0.8366 (t) REVERT: B 426 MET cc_start: 0.8867 (tpp) cc_final: 0.8580 (mmm) REVERT: B 500 ARG cc_start: 0.7694 (ptt90) cc_final: 0.7366 (tpm170) REVERT: B 536 THR cc_start: 0.8811 (m) cc_final: 0.8582 (p) REVERT: B 571 TRP cc_start: 0.7558 (m100) cc_final: 0.7161 (m100) REVERT: C 33 ASP cc_start: 0.8137 (m-30) cc_final: 0.7612 (t0) REVERT: C 108 LEU cc_start: 0.6949 (tp) cc_final: 0.6597 (tt) REVERT: D 74 THR cc_start: 0.8548 (m) cc_final: 0.8241 (p) REVERT: E 84 MET cc_start: 0.8162 (ttp) cc_final: 0.7931 (ttm) REVERT: E 207 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8242 (tmtt) REVERT: E 387 THR cc_start: 0.8889 (p) cc_final: 0.8469 (t) REVERT: E 426 MET cc_start: 0.8787 (tpp) cc_final: 0.8258 (mmm) REVERT: E 530 MET cc_start: 0.8908 (mtm) cc_final: 0.8686 (mtm) REVERT: E 536 THR cc_start: 0.8875 (m) cc_final: 0.8658 (p) REVERT: E 571 TRP cc_start: 0.7778 (m100) cc_final: 0.7182 (m100) REVERT: F 33 ASP cc_start: 0.8150 (m-30) cc_final: 0.7648 (t0) REVERT: F 108 LEU cc_start: 0.6900 (tp) cc_final: 0.6563 (tt) REVERT: G 74 THR cc_start: 0.8542 (m) cc_final: 0.8228 (p) outliers start: 9 outliers final: 3 residues processed: 526 average time/residue: 0.1584 time to fit residues: 121.8147 Evaluate side-chains 279 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain E residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 2 GLN B 540 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 2 GLN E 195 ASN E 352 HIS E 540 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082583 restraints weight = 51204.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083091 restraints weight = 35011.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084101 restraints weight = 26029.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.084627 restraints weight = 21230.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084751 restraints weight = 19365.275| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20877 Z= 0.178 Angle : 0.837 9.751 28587 Z= 0.410 Chirality : 0.050 0.331 3564 Planarity : 0.004 0.031 3372 Dihedral : 10.652 76.897 5340 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 8.28 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.12 (0.17), residues: 2325 helix: -0.05 (0.24), residues: 423 sheet: 0.47 (0.19), residues: 630 loop : 0.05 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 24 TYR 0.020 0.002 TYR D 92 PHE 0.017 0.002 PHE D 98 TRP 0.028 0.002 TRP A 479 HIS 0.015 0.002 HIS C 100I Details of bonding type rmsd covalent geometry : bond 0.00388 (20703) covalent geometry : angle 0.79317 (28104) SS BOND : bond 0.00261 ( 39) SS BOND : angle 0.90689 ( 78) hydrogen bonds : bond 0.05210 ( 776) hydrogen bonds : angle 7.13929 ( 2112) link_ALPHA1-3 : bond 0.00985 ( 6) link_ALPHA1-3 : angle 2.90823 ( 18) link_ALPHA1-6 : bond 0.00879 ( 6) link_ALPHA1-6 : angle 1.93213 ( 18) link_BETA1-4 : bond 0.00510 ( 54) link_BETA1-4 : angle 2.16329 ( 162) link_BETA1-6 : bond 0.00131 ( 3) link_BETA1-6 : angle 1.75081 ( 9) link_NAG-ASN : bond 0.00454 ( 66) link_NAG-ASN : angle 2.55977 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 0.640 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 104 MET cc_start: 0.8905 (ttp) cc_final: 0.8421 (tpt) REVERT: A 207 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7997 (tmtt) REVERT: A 309 ILE cc_start: 0.9229 (pt) cc_final: 0.8998 (mm) REVERT: A 387 THR cc_start: 0.8602 (p) cc_final: 0.8161 (t) REVERT: A 426 MET cc_start: 0.7954 (tpp) cc_final: 0.7423 (mmm) REVERT: H 2 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: H 20 LEU cc_start: 0.8420 (tp) cc_final: 0.8214 (tp) REVERT: H 31 TRP cc_start: 0.7513 (m-10) cc_final: 0.6960 (m-10) REVERT: H 108 LEU cc_start: 0.7267 (tp) cc_final: 0.6883 (tt) REVERT: L 49 TYR cc_start: 0.7042 (m-80) cc_final: 0.6637 (m-80) REVERT: L 87 TYR cc_start: 0.4691 (m-80) cc_final: 0.4434 (m-80) REVERT: L 95 ASP cc_start: 0.7262 (t0) cc_final: 0.6825 (t0) REVERT: L 96 PHE cc_start: 0.7721 (m-80) cc_final: 0.7288 (m-10) REVERT: B 207 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7886 (tmtt) REVERT: B 387 THR cc_start: 0.8557 (p) cc_final: 0.8103 (t) REVERT: B 426 MET cc_start: 0.8064 (tpp) cc_final: 0.7782 (mmm) REVERT: B 651 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7771 (t0) REVERT: C 48 ILE cc_start: 0.6774 (mt) cc_final: 0.6573 (mt) REVERT: C 66 ARG cc_start: 0.7887 (ttm110) cc_final: 0.7570 (ttm110) REVERT: C 100 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8162 (ttpp) REVERT: C 102 LEU cc_start: 0.8182 (mm) cc_final: 0.7970 (mm) REVERT: C 108 LEU cc_start: 0.7129 (tp) cc_final: 0.6699 (tt) REVERT: D 27 GLU cc_start: 0.5520 (mt-10) cc_final: 0.5183 (mp0) REVERT: E 207 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8065 (tmtt) REVERT: E 387 THR cc_start: 0.8611 (p) cc_final: 0.8212 (t) REVERT: E 426 MET cc_start: 0.8104 (tpp) cc_final: 0.7760 (mmm) REVERT: F 31 TRP cc_start: 0.7717 (m-10) cc_final: 0.7049 (m-10) REVERT: G 19 VAL cc_start: 0.7390 (t) cc_final: 0.6843 (t) REVERT: G 37 GLN cc_start: 0.8003 (tt0) cc_final: 0.7463 (tt0) REVERT: G 87 TYR cc_start: 0.4272 (m-80) cc_final: 0.3680 (m-80) outliers start: 60 outliers final: 17 residues processed: 377 average time/residue: 0.1434 time to fit residues: 82.0305 Evaluate side-chains 266 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 231 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 61 optimal weight: 0.0770 chunk 122 optimal weight: 7.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN A 652 GLN H 2 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 2 GLN C 80 GLN C 101 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN E 652 GLN F 2 GLN F 101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081090 restraints weight = 52007.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081864 restraints weight = 36198.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082996 restraints weight = 25399.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084365 restraints weight = 21097.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084566 restraints weight = 18310.839| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20877 Z= 0.156 Angle : 0.750 8.688 28587 Z= 0.364 Chirality : 0.048 0.263 3564 Planarity : 0.004 0.032 3372 Dihedral : 9.546 72.483 5334 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.04 % Allowed : 10.00 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.04 (0.17), residues: 2325 helix: 0.36 (0.26), residues: 420 sheet: 0.43 (0.19), residues: 669 loop : -0.23 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 24 TYR 0.017 0.002 TYR G 49 PHE 0.025 0.003 PHE L 71 TRP 0.016 0.002 TRP A 479 HIS 0.006 0.001 HIS H 100I Details of bonding type rmsd covalent geometry : bond 0.00347 (20703) covalent geometry : angle 0.71092 (28104) SS BOND : bond 0.00237 ( 39) SS BOND : angle 1.03244 ( 78) hydrogen bonds : bond 0.04640 ( 776) hydrogen bonds : angle 6.77971 ( 2112) link_ALPHA1-3 : bond 0.00980 ( 6) link_ALPHA1-3 : angle 2.12847 ( 18) link_ALPHA1-6 : bond 0.00881 ( 6) link_ALPHA1-6 : angle 1.69475 ( 18) link_BETA1-4 : bond 0.00472 ( 54) link_BETA1-4 : angle 1.77570 ( 162) link_BETA1-6 : bond 0.00083 ( 3) link_BETA1-6 : angle 1.67592 ( 9) link_NAG-ASN : bond 0.00371 ( 66) link_NAG-ASN : angle 2.38823 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 0.597 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 104 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8489 (tpt) REVERT: A 207 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7980 (tmtt) REVERT: A 309 ILE cc_start: 0.9266 (pt) cc_final: 0.9021 (mm) REVERT: A 387 THR cc_start: 0.8719 (p) cc_final: 0.8233 (t) REVERT: A 426 MET cc_start: 0.8038 (tpp) cc_final: 0.7464 (mmm) REVERT: H 20 LEU cc_start: 0.8524 (tp) cc_final: 0.8314 (tp) REVERT: H 67 LEU cc_start: 0.7302 (tp) cc_final: 0.6717 (mt) REVERT: H 108 LEU cc_start: 0.7325 (tp) cc_final: 0.6952 (tt) REVERT: L 49 TYR cc_start: 0.7378 (m-80) cc_final: 0.7028 (m-80) REVERT: L 73 LEU cc_start: 0.6864 (tp) cc_final: 0.6581 (tt) REVERT: L 87 TYR cc_start: 0.4765 (m-80) cc_final: 0.4464 (m-80) REVERT: B 207 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7663 (tptp) REVERT: B 387 THR cc_start: 0.8664 (p) cc_final: 0.8174 (t) REVERT: B 426 MET cc_start: 0.7971 (tpp) cc_final: 0.7551 (mmm) REVERT: C 81 MET cc_start: 0.6844 (tpp) cc_final: 0.6634 (tpp) REVERT: D 24 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8320 (mmm-85) REVERT: D 70 GLN cc_start: 0.7798 (tp-100) cc_final: 0.6696 (pp30) REVERT: E 104 MET cc_start: 0.8971 (ttt) cc_final: 0.8711 (tpp) REVERT: E 207 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7943 (tmtt) REVERT: E 387 THR cc_start: 0.8688 (p) cc_final: 0.8231 (t) REVERT: E 620 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6560 (t0) REVERT: F 33 ASP cc_start: 0.7991 (m-30) cc_final: 0.7424 (m-30) REVERT: G 4 MET cc_start: 0.5690 (ttp) cc_final: 0.5466 (ttp) REVERT: G 87 TYR cc_start: 0.4494 (m-80) cc_final: 0.3864 (m-80) outliers start: 62 outliers final: 29 residues processed: 309 average time/residue: 0.1464 time to fit residues: 68.3229 Evaluate side-chains 268 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 61 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN H 2 GLN B 287 HIS B 300 ASN B 651 ASN C 61 ASN E 287 HIS E 651 ASN F 2 GLN F 101 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.076811 restraints weight = 52864.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077847 restraints weight = 34968.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078886 restraints weight = 24744.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080130 restraints weight = 20813.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.080327 restraints weight = 18164.899| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20877 Z= 0.236 Angle : 0.784 8.742 28587 Z= 0.380 Chirality : 0.049 0.290 3564 Planarity : 0.005 0.052 3372 Dihedral : 8.837 66.983 5334 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.68 % Allowed : 10.39 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.16 (0.17), residues: 2325 helix: 0.18 (0.26), residues: 420 sheet: 0.28 (0.19), residues: 666 loop : -0.34 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.016 0.002 TYR L 90 PHE 0.022 0.003 PHE A 376 TRP 0.019 0.002 TRP E 571 HIS 0.008 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00532 (20703) covalent geometry : angle 0.74993 (28104) SS BOND : bond 0.00349 ( 39) SS BOND : angle 1.22227 ( 78) hydrogen bonds : bond 0.04420 ( 776) hydrogen bonds : angle 6.54944 ( 2112) link_ALPHA1-3 : bond 0.00864 ( 6) link_ALPHA1-3 : angle 2.39470 ( 18) link_ALPHA1-6 : bond 0.00921 ( 6) link_ALPHA1-6 : angle 1.91810 ( 18) link_BETA1-4 : bond 0.00403 ( 54) link_BETA1-4 : angle 1.68109 ( 162) link_BETA1-6 : bond 0.00287 ( 3) link_BETA1-6 : angle 1.96083 ( 9) link_NAG-ASN : bond 0.00488 ( 66) link_NAG-ASN : angle 2.22307 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 250 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8377 (tpt) REVERT: A 207 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7743 (tptp) REVERT: A 387 THR cc_start: 0.8893 (p) cc_final: 0.8418 (t) REVERT: A 629 MET cc_start: 0.8933 (mmm) cc_final: 0.8132 (mmm) REVERT: H 35 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7382 (mmp) REVERT: L 74 THR cc_start: 0.8070 (p) cc_final: 0.7830 (p) REVERT: L 87 TYR cc_start: 0.5126 (m-80) cc_final: 0.4625 (m-80) REVERT: L 95 ASP cc_start: 0.7777 (t0) cc_final: 0.7264 (t70) REVERT: B 84 MET cc_start: 0.7723 (tmm) cc_final: 0.7085 (tmm) REVERT: B 104 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8889 (ttp) REVERT: B 207 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7742 (tptm) REVERT: B 387 THR cc_start: 0.8789 (p) cc_final: 0.8389 (t) REVERT: B 475 MET cc_start: 0.8690 (mmm) cc_final: 0.8149 (mmm) REVERT: B 629 MET cc_start: 0.8889 (mmm) cc_final: 0.8433 (mmt) REVERT: B 651 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.8006 (t0) REVERT: C 2 GLN cc_start: 0.7931 (pm20) cc_final: 0.7422 (pp30) REVERT: C 33 ASP cc_start: 0.8080 (m-30) cc_final: 0.7648 (m-30) REVERT: C 79 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7011 (mt) REVERT: C 81 MET cc_start: 0.6985 (tpp) cc_final: 0.6710 (tpp) REVERT: D 70 GLN cc_start: 0.7892 (tp-100) cc_final: 0.6759 (pp30) REVERT: D 71 PHE cc_start: 0.8637 (m-80) cc_final: 0.8227 (m-80) REVERT: D 73 LEU cc_start: 0.6860 (tp) cc_final: 0.6621 (tt) REVERT: E 104 MET cc_start: 0.9045 (ttt) cc_final: 0.8809 (tpp) REVERT: E 207 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7678 (tmtt) REVERT: E 387 THR cc_start: 0.8735 (p) cc_final: 0.8348 (t) REVERT: E 500 ARG cc_start: 0.4953 (tpt170) cc_final: 0.4599 (tpm170) REVERT: E 620 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6548 (t0) REVERT: E 629 MET cc_start: 0.8881 (mmm) cc_final: 0.8115 (mmm) REVERT: F 67 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.6980 (mt) REVERT: G 63 LYS cc_start: 0.7279 (tptp) cc_final: 0.6881 (mptt) REVERT: G 87 TYR cc_start: 0.4920 (m-80) cc_final: 0.4413 (m-80) outliers start: 75 outliers final: 35 residues processed: 302 average time/residue: 0.1521 time to fit residues: 69.8551 Evaluate side-chains 265 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 107 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 651 ASN H 2 GLN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 101 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.074944 restraints weight = 53743.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076243 restraints weight = 35290.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.077098 restraints weight = 24855.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078435 restraints weight = 21280.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078484 restraints weight = 18763.942| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20877 Z= 0.266 Angle : 0.821 10.013 28587 Z= 0.396 Chirality : 0.050 0.305 3564 Planarity : 0.004 0.054 3372 Dihedral : 8.711 64.210 5334 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.94 % Allowed : 10.93 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.31 (0.17), residues: 2325 helix: 0.10 (0.26), residues: 417 sheet: 0.31 (0.20), residues: 660 loop : -0.54 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 66 TYR 0.019 0.002 TYR C 59 PHE 0.024 0.003 PHE L 71 TRP 0.025 0.002 TRP F 62 HIS 0.008 0.002 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00608 (20703) covalent geometry : angle 0.77930 (28104) SS BOND : bond 0.00434 ( 39) SS BOND : angle 1.60351 ( 78) hydrogen bonds : bond 0.04482 ( 776) hydrogen bonds : angle 6.45595 ( 2112) link_ALPHA1-3 : bond 0.00707 ( 6) link_ALPHA1-3 : angle 2.50982 ( 18) link_ALPHA1-6 : bond 0.00970 ( 6) link_ALPHA1-6 : angle 1.85698 ( 18) link_BETA1-4 : bond 0.00385 ( 54) link_BETA1-4 : angle 1.65544 ( 162) link_BETA1-6 : bond 0.00362 ( 3) link_BETA1-6 : angle 1.95634 ( 9) link_NAG-ASN : bond 0.00526 ( 66) link_NAG-ASN : angle 2.61725 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8357 (tpt) REVERT: A 207 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7665 (tptp) REVERT: A 387 THR cc_start: 0.9009 (p) cc_final: 0.8526 (t) REVERT: A 629 MET cc_start: 0.9016 (mmm) cc_final: 0.8355 (mmm) REVERT: H 35 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7228 (mmp) REVERT: H 67 LEU cc_start: 0.7658 (tp) cc_final: 0.7084 (mt) REVERT: H 102 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7759 (mm) REVERT: L 4 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5540 (mtp) REVERT: L 63 LYS cc_start: 0.7622 (tptp) cc_final: 0.7202 (mptt) REVERT: L 87 TYR cc_start: 0.5300 (m-80) cc_final: 0.4847 (m-80) REVERT: L 95 ASP cc_start: 0.7974 (t0) cc_final: 0.7395 (t70) REVERT: B 84 MET cc_start: 0.7719 (tmm) cc_final: 0.7096 (tmm) REVERT: B 104 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8819 (tpp) REVERT: B 207 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7911 (tptm) REVERT: B 387 THR cc_start: 0.8823 (p) cc_final: 0.8352 (t) REVERT: B 475 MET cc_start: 0.8676 (mmm) cc_final: 0.8455 (mmm) REVERT: B 629 MET cc_start: 0.9003 (mmm) cc_final: 0.8517 (mmm) REVERT: B 650 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: C 2 GLN cc_start: 0.7860 (pm20) cc_final: 0.6795 (pp30) REVERT: C 33 ASP cc_start: 0.8150 (m-30) cc_final: 0.7712 (m-30) REVERT: C 35 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7564 (mmp) REVERT: C 66 ARG cc_start: 0.7164 (ttp-110) cc_final: 0.6810 (ttp-110) REVERT: C 81 MET cc_start: 0.7184 (tpp) cc_final: 0.6909 (tpp) REVERT: D 4 MET cc_start: 0.6127 (ttp) cc_final: 0.5692 (ttm) REVERT: D 24 ARG cc_start: 0.8752 (mmm-85) cc_final: 0.8542 (mmm-85) REVERT: D 63 LYS cc_start: 0.7569 (tptp) cc_final: 0.7310 (mptt) REVERT: D 70 GLN cc_start: 0.7797 (tp-100) cc_final: 0.6834 (pp30) REVERT: D 71 PHE cc_start: 0.8686 (m-80) cc_final: 0.8275 (m-80) REVERT: D 73 LEU cc_start: 0.6964 (tp) cc_final: 0.6750 (tt) REVERT: D 87 TYR cc_start: 0.5693 (m-80) cc_final: 0.5352 (m-80) REVERT: D 92 TYR cc_start: 0.7686 (t80) cc_final: 0.7433 (t80) REVERT: E 104 MET cc_start: 0.9044 (ttt) cc_final: 0.8793 (tpp) REVERT: E 207 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7806 (tmtt) REVERT: E 387 THR cc_start: 0.8847 (p) cc_final: 0.8409 (t) REVERT: E 629 MET cc_start: 0.8997 (mmm) cc_final: 0.8344 (mmm) REVERT: E 650 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: F 62 TRP cc_start: 0.7791 (t60) cc_final: 0.7399 (t60) REVERT: F 67 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6813 (mt) REVERT: F 81 MET cc_start: 0.7223 (tpp) cc_final: 0.6902 (tpp) REVERT: G 63 LYS cc_start: 0.7251 (tptp) cc_final: 0.6959 (mptt) REVERT: G 87 TYR cc_start: 0.5373 (m-80) cc_final: 0.5010 (m-80) outliers start: 60 outliers final: 38 residues processed: 282 average time/residue: 0.1480 time to fit residues: 64.2999 Evaluate side-chains 267 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 227 optimal weight: 0.0470 chunk 100 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN F 101 ASN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072393 restraints weight = 54292.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073516 restraints weight = 36728.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.074294 restraints weight = 26430.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075387 restraints weight = 23103.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075523 restraints weight = 20007.657| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 20877 Z= 0.365 Angle : 0.938 10.173 28587 Z= 0.450 Chirality : 0.053 0.340 3564 Planarity : 0.005 0.051 3372 Dihedral : 9.189 62.702 5334 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.53 % Allowed : 10.83 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.80 (0.17), residues: 2325 helix: -0.37 (0.25), residues: 417 sheet: 0.05 (0.19), residues: 666 loop : -0.87 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 192 TYR 0.019 0.003 TYR B 217 PHE 0.023 0.003 PHE L 71 TRP 0.032 0.003 TRP A 571 HIS 0.012 0.003 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00837 (20703) covalent geometry : angle 0.89519 (28104) SS BOND : bond 0.00573 ( 39) SS BOND : angle 1.65659 ( 78) hydrogen bonds : bond 0.04839 ( 776) hydrogen bonds : angle 6.64315 ( 2112) link_ALPHA1-3 : bond 0.00532 ( 6) link_ALPHA1-3 : angle 2.87247 ( 18) link_ALPHA1-6 : bond 0.00873 ( 6) link_ALPHA1-6 : angle 1.88007 ( 18) link_BETA1-4 : bond 0.00470 ( 54) link_BETA1-4 : angle 1.90005 ( 162) link_BETA1-6 : bond 0.00587 ( 3) link_BETA1-6 : angle 2.12870 ( 9) link_NAG-ASN : bond 0.00668 ( 66) link_NAG-ASN : angle 2.82794 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8598 (tpt) REVERT: A 207 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7802 (tptp) REVERT: A 650 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: H 2 GLN cc_start: 0.7845 (pm20) cc_final: 0.7536 (pm20) REVERT: H 35 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7141 (mmp) REVERT: H 71 LYS cc_start: 0.6897 (ttpt) cc_final: 0.6152 (ptpp) REVERT: H 80 GLN cc_start: 0.8331 (mp10) cc_final: 0.7995 (mp10) REVERT: L 4 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5918 (mtp) REVERT: L 27 GLU cc_start: 0.5801 (mp0) cc_final: 0.5321 (mp0) REVERT: L 87 TYR cc_start: 0.5803 (m-80) cc_final: 0.5471 (m-80) REVERT: L 95 ASP cc_start: 0.8081 (t0) cc_final: 0.7661 (t70) REVERT: B 84 MET cc_start: 0.7819 (tmm) cc_final: 0.7195 (tmm) REVERT: B 104 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8836 (ttp) REVERT: B 207 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8046 (tptm) REVERT: B 629 MET cc_start: 0.9121 (mmm) cc_final: 0.8646 (mmm) REVERT: C 66 ARG cc_start: 0.7313 (ttp-110) cc_final: 0.6937 (ttp-110) REVERT: D 4 MET cc_start: 0.5998 (ttp) cc_final: 0.5646 (ttm) REVERT: D 24 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8338 (mmm-85) REVERT: D 63 LYS cc_start: 0.7713 (tptp) cc_final: 0.7403 (mppt) REVERT: D 70 GLN cc_start: 0.7897 (tp-100) cc_final: 0.6948 (pp30) REVERT: D 71 PHE cc_start: 0.8724 (m-80) cc_final: 0.8393 (m-80) REVERT: E 207 LYS cc_start: 0.8507 (mmtt) cc_final: 0.7841 (tmtt) REVERT: E 500 ARG cc_start: 0.5151 (tpt170) cc_final: 0.4900 (tpm170) REVERT: E 530 MET cc_start: 0.9080 (mtm) cc_final: 0.8616 (ttm) REVERT: E 629 MET cc_start: 0.9037 (mmm) cc_final: 0.8509 (mmm) REVERT: E 650 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: F 47 TRP cc_start: 0.6763 (t-100) cc_final: 0.6562 (t-100) REVERT: G 63 LYS cc_start: 0.7596 (tptp) cc_final: 0.7228 (mptt) REVERT: G 87 TYR cc_start: 0.5701 (m-80) cc_final: 0.5392 (m-80) outliers start: 72 outliers final: 47 residues processed: 277 average time/residue: 0.1456 time to fit residues: 61.6585 Evaluate side-chains 264 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 135 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 156 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.073952 restraints weight = 53822.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.075219 restraints weight = 36056.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075997 restraints weight = 25673.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.077029 restraints weight = 22678.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077170 restraints weight = 19390.653| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 20877 Z= 0.236 Angle : 0.807 10.021 28587 Z= 0.387 Chirality : 0.049 0.318 3564 Planarity : 0.004 0.070 3372 Dihedral : 8.803 59.915 5334 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.43 % Allowed : 11.76 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.77 (0.17), residues: 2325 helix: -0.25 (0.26), residues: 423 sheet: 0.04 (0.19), residues: 690 loop : -0.88 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 24 TYR 0.024 0.002 TYR L 49 PHE 0.026 0.003 PHE L 71 TRP 0.034 0.002 TRP F 62 HIS 0.007 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00543 (20703) covalent geometry : angle 0.76430 (28104) SS BOND : bond 0.00403 ( 39) SS BOND : angle 1.45495 ( 78) hydrogen bonds : bond 0.04372 ( 776) hydrogen bonds : angle 6.42797 ( 2112) link_ALPHA1-3 : bond 0.00666 ( 6) link_ALPHA1-3 : angle 2.47227 ( 18) link_ALPHA1-6 : bond 0.00791 ( 6) link_ALPHA1-6 : angle 1.68244 ( 18) link_BETA1-4 : bond 0.00357 ( 54) link_BETA1-4 : angle 1.73042 ( 162) link_BETA1-6 : bond 0.00557 ( 3) link_BETA1-6 : angle 2.16941 ( 9) link_NAG-ASN : bond 0.00492 ( 66) link_NAG-ASN : angle 2.62756 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8486 (tpt) REVERT: A 207 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7703 (tptp) REVERT: A 475 MET cc_start: 0.8604 (mmt) cc_final: 0.8342 (mmt) REVERT: A 629 MET cc_start: 0.9171 (mmm) cc_final: 0.8399 (mmm) REVERT: A 650 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: H 35 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7240 (mmp) REVERT: H 58 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7436 (p90) REVERT: H 71 LYS cc_start: 0.6889 (ttpt) cc_final: 0.6136 (ptpp) REVERT: H 80 GLN cc_start: 0.8257 (mp10) cc_final: 0.7959 (mp10) REVERT: L 4 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5914 (ttm) REVERT: L 63 LYS cc_start: 0.7640 (tptp) cc_final: 0.7310 (mppt) REVERT: L 87 TYR cc_start: 0.5749 (m-80) cc_final: 0.5330 (m-80) REVERT: L 95 ASP cc_start: 0.7895 (t0) cc_final: 0.7662 (t70) REVERT: B 84 MET cc_start: 0.7785 (tmm) cc_final: 0.7393 (tmm) REVERT: B 104 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8812 (ttp) REVERT: B 207 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7940 (tptm) REVERT: B 629 MET cc_start: 0.8992 (mmm) cc_final: 0.8729 (mmm) REVERT: B 650 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: C 71 LYS cc_start: 0.6879 (ttpt) cc_final: 0.5952 (ptpp) REVERT: D 4 MET cc_start: 0.5874 (ttp) cc_final: 0.5555 (ttm) REVERT: D 27 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: D 63 LYS cc_start: 0.7682 (tptp) cc_final: 0.7454 (mppt) REVERT: D 70 GLN cc_start: 0.7789 (tp-100) cc_final: 0.7037 (pp30) REVERT: E 207 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7861 (tmtt) REVERT: E 530 MET cc_start: 0.8989 (mtm) cc_final: 0.8539 (ttm) REVERT: E 536 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9184 (m) REVERT: E 629 MET cc_start: 0.8942 (mmm) cc_final: 0.8557 (mmm) REVERT: E 650 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: F 47 TRP cc_start: 0.6876 (t-100) cc_final: 0.6649 (t-100) REVERT: F 100 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7791 (ttpp) REVERT: G 63 LYS cc_start: 0.7626 (tptp) cc_final: 0.7344 (mptt) outliers start: 70 outliers final: 47 residues processed: 271 average time/residue: 0.1496 time to fit residues: 61.8303 Evaluate side-chains 269 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 2 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.077093 restraints weight = 52952.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.078478 restraints weight = 35610.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079395 restraints weight = 24796.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080587 restraints weight = 20640.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080720 restraints weight = 18165.162| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 20877 Z= 0.134 Angle : 0.725 10.561 28587 Z= 0.349 Chirality : 0.047 0.275 3564 Planarity : 0.004 0.062 3372 Dihedral : 8.069 57.780 5334 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.70 % Allowed : 12.89 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2325 helix: 0.47 (0.27), residues: 399 sheet: 0.16 (0.19), residues: 693 loop : -0.79 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 66 TYR 0.019 0.001 TYR L 49 PHE 0.024 0.002 PHE L 71 TRP 0.024 0.002 TRP H 47 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00304 (20703) covalent geometry : angle 0.68261 (28104) SS BOND : bond 0.00314 ( 39) SS BOND : angle 1.44102 ( 78) hydrogen bonds : bond 0.03978 ( 776) hydrogen bonds : angle 6.17470 ( 2112) link_ALPHA1-3 : bond 0.00837 ( 6) link_ALPHA1-3 : angle 1.98228 ( 18) link_ALPHA1-6 : bond 0.00779 ( 6) link_ALPHA1-6 : angle 1.73313 ( 18) link_BETA1-4 : bond 0.00390 ( 54) link_BETA1-4 : angle 1.60583 ( 162) link_BETA1-6 : bond 0.00211 ( 3) link_BETA1-6 : angle 2.01040 ( 9) link_NAG-ASN : bond 0.00444 ( 66) link_NAG-ASN : angle 2.44572 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8484 (tpt) REVERT: A 207 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7708 (tptp) REVERT: A 475 MET cc_start: 0.8545 (mmt) cc_final: 0.8299 (mmt) REVERT: A 629 MET cc_start: 0.9108 (mmm) cc_final: 0.8424 (mmm) REVERT: A 650 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: H 2 GLN cc_start: 0.7774 (pm20) cc_final: 0.7563 (pm20) REVERT: H 35 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7101 (mmp) REVERT: H 47 TRP cc_start: 0.6575 (t-100) cc_final: 0.6138 (t-100) REVERT: H 80 GLN cc_start: 0.8247 (mp10) cc_final: 0.8004 (mp10) REVERT: H 100 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8092 (ttpp) REVERT: L 27 GLU cc_start: 0.6129 (mp0) cc_final: 0.5836 (mp0) REVERT: L 63 LYS cc_start: 0.7663 (tptp) cc_final: 0.7309 (mptt) REVERT: L 87 TYR cc_start: 0.5616 (m-80) cc_final: 0.5148 (m-80) REVERT: L 95 ASP cc_start: 0.7841 (t0) cc_final: 0.7598 (t70) REVERT: B 207 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7839 (tmtt) REVERT: B 629 MET cc_start: 0.8870 (mmm) cc_final: 0.8649 (mmm) REVERT: B 650 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: C 2 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6840 (pp30) REVERT: C 102 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8171 (mm) REVERT: D 4 MET cc_start: 0.5754 (ttp) cc_final: 0.5504 (ttm) REVERT: D 24 ARG cc_start: 0.8688 (mmm-85) cc_final: 0.8339 (mmm-85) REVERT: D 63 LYS cc_start: 0.7660 (tptp) cc_final: 0.7433 (mppt) REVERT: D 70 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7052 (pp30) REVERT: D 87 TYR cc_start: 0.5846 (m-80) cc_final: 0.5495 (m-80) REVERT: E 104 MET cc_start: 0.8976 (tpp) cc_final: 0.8665 (tpt) REVERT: E 207 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7835 (tmtt) REVERT: E 530 MET cc_start: 0.8910 (mtm) cc_final: 0.8677 (ttm) REVERT: E 629 MET cc_start: 0.8815 (mmm) cc_final: 0.8611 (mmm) REVERT: E 650 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: F 47 TRP cc_start: 0.6800 (t-100) cc_final: 0.6565 (t-100) REVERT: F 100 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7717 (ttpt) outliers start: 55 outliers final: 34 residues processed: 265 average time/residue: 0.1512 time to fit residues: 60.9075 Evaluate side-chains 261 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 203 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 101 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.097309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074502 restraints weight = 53769.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.075715 restraints weight = 35524.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076541 restraints weight = 25436.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077275 restraints weight = 21693.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077431 restraints weight = 19897.538| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 20877 Z= 0.241 Angle : 0.807 12.308 28587 Z= 0.384 Chirality : 0.049 0.401 3564 Planarity : 0.005 0.082 3372 Dihedral : 8.046 58.030 5334 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.75 % Allowed : 12.75 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.60 (0.17), residues: 2325 helix: 0.25 (0.26), residues: 408 sheet: 0.15 (0.19), residues: 690 loop : -0.92 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.020 0.002 TYR L 49 PHE 0.024 0.003 PHE L 71 TRP 0.028 0.002 TRP A 571 HIS 0.008 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00556 (20703) covalent geometry : angle 0.76099 (28104) SS BOND : bond 0.00452 ( 39) SS BOND : angle 1.76295 ( 78) hydrogen bonds : bond 0.04198 ( 776) hydrogen bonds : angle 6.25044 ( 2112) link_ALPHA1-3 : bond 0.00600 ( 6) link_ALPHA1-3 : angle 2.41648 ( 18) link_ALPHA1-6 : bond 0.00732 ( 6) link_ALPHA1-6 : angle 1.77886 ( 18) link_BETA1-4 : bond 0.00390 ( 54) link_BETA1-4 : angle 1.75621 ( 162) link_BETA1-6 : bond 0.00417 ( 3) link_BETA1-6 : angle 1.98003 ( 9) link_NAG-ASN : bond 0.00468 ( 66) link_NAG-ASN : angle 2.67088 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8522 (tpt) REVERT: A 207 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7761 (tptp) REVERT: A 629 MET cc_start: 0.9177 (mmm) cc_final: 0.8603 (mmm) REVERT: A 650 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: H 35 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7022 (mmp) REVERT: H 80 GLN cc_start: 0.8245 (mp10) cc_final: 0.7990 (mp10) REVERT: H 100 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8167 (ttpp) REVERT: L 27 GLU cc_start: 0.6340 (mp0) cc_final: 0.6042 (mp0) REVERT: L 63 LYS cc_start: 0.7660 (tptp) cc_final: 0.7358 (mppt) REVERT: L 87 TYR cc_start: 0.5762 (m-80) cc_final: 0.5335 (m-80) REVERT: L 95 ASP cc_start: 0.8015 (t0) cc_final: 0.7648 (t0) REVERT: B 84 MET cc_start: 0.7715 (tmm) cc_final: 0.7422 (tmm) REVERT: B 207 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7904 (tmtt) REVERT: B 342 LEU cc_start: 0.9418 (mp) cc_final: 0.9022 (mt) REVERT: B 629 MET cc_start: 0.8957 (mmm) cc_final: 0.8685 (mmm) REVERT: B 650 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: D 63 LYS cc_start: 0.7722 (tptp) cc_final: 0.7390 (mptt) REVERT: D 70 GLN cc_start: 0.7979 (tp-100) cc_final: 0.6920 (pp30) REVERT: E 104 MET cc_start: 0.8829 (tpp) cc_final: 0.8557 (tpt) REVERT: E 207 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7795 (tptp) REVERT: E 530 MET cc_start: 0.9009 (mtm) cc_final: 0.8720 (ttm) REVERT: E 629 MET cc_start: 0.8919 (mmm) cc_final: 0.8597 (mmm) REVERT: E 650 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: F 47 TRP cc_start: 0.6735 (t-100) cc_final: 0.6491 (t-100) REVERT: F 100 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7739 (ttpt) REVERT: G 103 GLU cc_start: 0.6053 (mp0) cc_final: 0.5641 (mp0) outliers start: 56 outliers final: 41 residues processed: 250 average time/residue: 0.1546 time to fit residues: 58.8954 Evaluate side-chains 253 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain E residue 651 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 183 optimal weight: 5.9990 chunk 5 optimal weight: 0.1980 chunk 207 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 219 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN L 22 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 101 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078075 restraints weight = 53006.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079046 restraints weight = 36609.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080123 restraints weight = 25748.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081492 restraints weight = 21110.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081605 restraints weight = 18496.675| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20877 Z= 0.123 Angle : 0.719 11.240 28587 Z= 0.344 Chirality : 0.047 0.324 3564 Planarity : 0.004 0.070 3372 Dihedral : 7.573 55.718 5334 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.01 % Allowed : 13.24 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2325 helix: 0.67 (0.26), residues: 390 sheet: 0.10 (0.19), residues: 720 loop : -0.74 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 66 TYR 0.020 0.001 TYR D 92 PHE 0.022 0.002 PHE A 361 TRP 0.029 0.002 TRP H 47 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00279 (20703) covalent geometry : angle 0.67552 (28104) SS BOND : bond 0.00378 ( 39) SS BOND : angle 1.31052 ( 78) hydrogen bonds : bond 0.03792 ( 776) hydrogen bonds : angle 6.05420 ( 2112) link_ALPHA1-3 : bond 0.00811 ( 6) link_ALPHA1-3 : angle 1.80330 ( 18) link_ALPHA1-6 : bond 0.00849 ( 6) link_ALPHA1-6 : angle 1.74328 ( 18) link_BETA1-4 : bond 0.00418 ( 54) link_BETA1-4 : angle 1.58826 ( 162) link_BETA1-6 : bond 0.00216 ( 3) link_BETA1-6 : angle 1.88180 ( 9) link_NAG-ASN : bond 0.00548 ( 66) link_NAG-ASN : angle 2.51520 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8524 (tpt) REVERT: A 207 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7571 (tptp) REVERT: A 629 MET cc_start: 0.9008 (mmm) cc_final: 0.8554 (mmm) REVERT: A 650 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: H 20 LEU cc_start: 0.8695 (tp) cc_final: 0.8444 (tp) REVERT: H 35 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7021 (mmp) REVERT: H 47 TRP cc_start: 0.6473 (t-100) cc_final: 0.6197 (t-100) REVERT: H 100 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8375 (ttpp) REVERT: H 108 LEU cc_start: 0.7085 (tp) cc_final: 0.6603 (tt) REVERT: L 22 ASN cc_start: 0.6256 (OUTLIER) cc_final: 0.5937 (t0) REVERT: L 63 LYS cc_start: 0.7684 (tptp) cc_final: 0.7342 (mptt) REVERT: L 87 TYR cc_start: 0.5659 (m-80) cc_final: 0.5161 (m-80) REVERT: L 95 ASP cc_start: 0.7964 (t0) cc_final: 0.7438 (t0) REVERT: B 207 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7788 (tmtt) REVERT: B 650 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: C 100 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7978 (tmmt) REVERT: D 63 LYS cc_start: 0.7792 (tptp) cc_final: 0.7371 (mptt) REVERT: D 70 GLN cc_start: 0.7849 (tp-100) cc_final: 0.6907 (pp30) REVERT: D 87 TYR cc_start: 0.5840 (m-80) cc_final: 0.5496 (m-80) REVERT: E 104 MET cc_start: 0.8933 (tpp) cc_final: 0.8622 (tpt) REVERT: E 207 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7740 (tmtt) REVERT: E 530 MET cc_start: 0.8882 (mtm) cc_final: 0.8604 (ttm) REVERT: F 47 TRP cc_start: 0.6568 (t-100) cc_final: 0.6322 (t-100) REVERT: F 66 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.7310 (ttp80) REVERT: F 100 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7773 (ttpt) outliers start: 41 outliers final: 28 residues processed: 252 average time/residue: 0.1488 time to fit residues: 57.2561 Evaluate side-chains 249 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 3 optimal weight: 0.0050 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 2 GLN ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 101 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076339 restraints weight = 53610.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077884 restraints weight = 34414.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078614 restraints weight = 24501.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078955 restraints weight = 20862.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079062 restraints weight = 19324.431| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20877 Z= 0.173 Angle : 0.743 11.066 28587 Z= 0.356 Chirality : 0.047 0.319 3564 Planarity : 0.004 0.066 3372 Dihedral : 7.501 55.853 5334 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.30 % Allowed : 13.28 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.44 (0.17), residues: 2325 helix: 0.47 (0.26), residues: 408 sheet: 0.12 (0.19), residues: 729 loop : -0.78 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 66 TYR 0.019 0.002 TYR D 92 PHE 0.027 0.002 PHE A 361 TRP 0.026 0.002 TRP H 62 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00402 (20703) covalent geometry : angle 0.69711 (28104) SS BOND : bond 0.00362 ( 39) SS BOND : angle 1.47519 ( 78) hydrogen bonds : bond 0.03872 ( 776) hydrogen bonds : angle 6.06412 ( 2112) link_ALPHA1-3 : bond 0.00670 ( 6) link_ALPHA1-3 : angle 2.12178 ( 18) link_ALPHA1-6 : bond 0.00796 ( 6) link_ALPHA1-6 : angle 1.75872 ( 18) link_BETA1-4 : bond 0.00394 ( 54) link_BETA1-4 : angle 1.63148 ( 162) link_BETA1-6 : bond 0.00253 ( 3) link_BETA1-6 : angle 1.86692 ( 9) link_NAG-ASN : bond 0.00396 ( 66) link_NAG-ASN : angle 2.60738 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2841.89 seconds wall clock time: 50 minutes 21.08 seconds (3021.08 seconds total)