Starting phenix.real_space_refine on Sun Aug 24 14:38:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u59_20642/08_2025/6u59_20642.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u59_20642/08_2025/6u59_20642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u59_20642/08_2025/6u59_20642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u59_20642/08_2025/6u59_20642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u59_20642/08_2025/6u59_20642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u59_20642/08_2025/6u59_20642.map" } resolution = 3.86 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= 0.005 sd= 0.096 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 126 5.16 5 C 12780 2.51 5 N 3342 2.21 5 O 4191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20439 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "F" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "I" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "K" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.27, per 1000 atoms: 0.26 Number of scatterers: 20439 At special positions: 0 Unit cell: (152.95, 165.6, 124.2, 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 126 16.00 O 4191 8.00 N 3342 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.13 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.13 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.13 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.05 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " 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 W 3 " - " MAN W 4 " " BMA j 3 " - " MAN j 4 " " BMA w 3 " - " MAN w 4 " BETA1-4 " 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG 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-ASN " NAG A 601 " - " ASN A 88 " " NAG A 606 " - " ASN A 197 " " NAG A 613 " - " ASN A 301 " " NAG A 614 " - " ASN A 339 " " NAG A 618 " - " ASN A 355 " " NAG A 635 " - " ASN A 396 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 637 " " NAG B 704 " - " ASN B 611 " " NAG C 601 " - " ASN C 88 " " NAG C 606 " - " ASN C 197 " " NAG C 613 " - " ASN C 301 " " NAG C 614 " - " ASN C 339 " " NAG C 618 " - " ASN C 355 " " NAG C 635 " - " ASN C 396 " " NAG D 701 " - " ASN D 616 " " NAG D 702 " - " ASN D 625 " " NAG D 703 " - " ASN D 637 " " NAG D 704 " - " ASN D 611 " " NAG G 601 " - " ASN G 88 " " NAG G 606 " - " ASN G 197 " " NAG G 613 " - " ASN G 301 " " NAG G 614 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 635 " - " ASN G 396 " " NAG I 701 " - " ASN I 616 " " NAG I 702 " - " ASN I 625 " " NAG I 703 " - " ASN I 637 " " NAG I 704 " - " ASN I 611 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 362 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 241 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 160 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 295 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 362 " " NAG g 1 " - " ASN C 386 " " NAG h 1 " - " ASN C 392 " " NAG i 1 " - " ASN C 448 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 241 " " NAG l 1 " - " ASN C 413 " " NAG m 1 " - " ASN G 156 " " NAG n 1 " - " ASN G 160 " " NAG o 1 " - " ASN G 234 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 332 " " NAG s 1 " - " ASN G 362 " " NAG t 1 " - " ASN G 386 " " NAG u 1 " - " ASN G 392 " " NAG v 1 " - " ASN G 448 " " NAG w 1 " - " ASN G 262 " " NAG x 1 " - " ASN G 241 " " NAG y 1 " - " ASN G 413 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 855.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 18.9% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.587A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.790A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 530' Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 569 through 597 removed outlier: 4.037A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 651 through 662 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.587A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.791A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 530' Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 569 through 597 removed outlier: 4.037A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 648 Processing helix chain 'D' and resid 651 through 662 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 116 removed outlier: 3.586A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.790A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 526 through 530' Processing helix chain 'I' and resid 538 through 543 Processing helix chain 'I' and resid 569 through 597 removed outlier: 4.036A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 648 Processing helix chain 'I' and resid 651 through 662 Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) 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 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.430A 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: 10.312A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.790A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.841A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.111A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 23 removed outlier: 6.773A pdb=" N THR H 76 " --> pdb=" O THR H 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AC3, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.429A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.313A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.791A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 308 removed outlier: 6.842A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.112A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'F' and resid 18 through 23 removed outlier: 6.772A pdb=" N THR F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'G' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE G 215 " --> pdb=" O GLY G 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY G 250 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR G 217 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'G' and resid 169 through 176 Processing sheet with id=AD9, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.429A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 259 through 261 removed outlier: 10.312A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.790A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR G 357 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE G 468 " --> pdb=" O THR G 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE G 359 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 301 through 308 removed outlier: 6.842A pdb=" N ASN G 301 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE G 323 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY G 321 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS J 107 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS J 107 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.112A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 23 removed outlier: 6.772A pdb=" N THR K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 1980 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: 3.87 Time building geometry restraints manager: 2.57 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: 4960 1.32 - 1.46: 6549 1.46 - 1.59: 9164 1.59 - 1.73: 24 1.73 - 1.86: 156 Bond restraints: 20853 Sorted by residual: bond pdb=" CE1 HIS C 374 " pdb=" NE2 HIS C 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.84e+01 bond pdb=" CE1 HIS G 374 " pdb=" NE2 HIS G 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.80e+01 bond pdb=" CE1 HIS A 374 " pdb=" NE2 HIS A 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.76e+01 bond pdb=" CB HIS G 105 " pdb=" CG HIS G 105 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.61e+01 bond pdb=" CB HIS C 105 " pdb=" CG HIS C 105 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.61e+01 ... (remaining 20848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 24014 2.39 - 4.79: 3678 4.79 - 7.18: 611 7.18 - 9.58: 38 9.58 - 11.97: 12 Bond angle restraints: 28353 Sorted by residual: angle pdb=" N GLU A 370 " pdb=" CA GLU A 370 " pdb=" C GLU A 370 " ideal model delta sigma weight residual 114.62 102.65 11.97 1.14e+00 7.69e-01 1.10e+02 angle pdb=" N GLU G 370 " pdb=" CA GLU G 370 " pdb=" C GLU G 370 " ideal model delta sigma weight residual 114.62 102.69 11.93 1.14e+00 7.69e-01 1.09e+02 angle pdb=" N GLU C 370 " pdb=" CA GLU C 370 " pdb=" C GLU C 370 " ideal model delta sigma weight residual 114.62 102.70 11.92 1.14e+00 7.69e-01 1.09e+02 angle pdb=" N ILE I 602 " pdb=" CA ILE I 602 " pdb=" C ILE I 602 " ideal model delta sigma weight residual 111.67 103.88 7.79 9.50e-01 1.11e+00 6.72e+01 angle pdb=" N ILE B 602 " pdb=" CA ILE B 602 " pdb=" C ILE B 602 " ideal model delta sigma weight residual 111.67 103.89 7.78 9.50e-01 1.11e+00 6.70e+01 ... (remaining 28348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 13283 21.95 - 43.90: 454 43.90 - 65.85: 99 65.85 - 87.80: 42 87.80 - 109.75: 30 Dihedral angle restraints: 13908 sinusoidal: 6972 harmonic: 6936 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.59 32.59 1 1.00e+01 1.00e-02 1.51e+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 -118.58 32.58 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.56 32.56 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 13905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1736 0.065 - 0.130: 1062 0.130 - 0.195: 496 0.195 - 0.259: 181 0.259 - 0.324: 41 Chirality restraints: 3516 Sorted by residual: chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG y 2 " pdb=" O4 NAG y 1 " pdb=" C2 NAG y 2 " pdb=" O5 NAG y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 ... (remaining 3513 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 107 " 0.040 2.00e-02 2.50e+03 8.11e-02 6.58e+01 pdb=" C LYS J 107 " -0.140 2.00e-02 2.50e+03 pdb=" O LYS J 107 " 0.051 2.00e-02 2.50e+03 pdb=" OXT LYS J 107 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 107 " -0.040 2.00e-02 2.50e+03 8.10e-02 6.57e+01 pdb=" C LYS E 107 " 0.140 2.00e-02 2.50e+03 pdb=" O LYS E 107 " -0.051 2.00e-02 2.50e+03 pdb=" OXT LYS E 107 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 107 " 0.040 2.00e-02 2.50e+03 8.09e-02 6.55e+01 pdb=" C LYS L 107 " -0.140 2.00e-02 2.50e+03 pdb=" O LYS L 107 " 0.051 2.00e-02 2.50e+03 pdb=" OXT LYS L 107 " 0.049 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4375 2.77 - 3.30: 18449 3.30 - 3.83: 34553 3.83 - 4.37: 40023 4.37 - 4.90: 65587 Nonbonded interactions: 162987 Sorted by model distance: nonbonded pdb=" O4 NAG k 2 " pdb=" O6 NAG k 2 " model vdw 2.234 3.040 nonbonded pdb=" O4 NAG X 2 " pdb=" O6 NAG X 2 " model vdw 2.234 3.040 nonbonded pdb=" O4 NAG x 2 " pdb=" O6 NAG x 2 " model vdw 2.234 3.040 nonbonded pdb=" O4 NAG f 2 " pdb=" O6 NAG f 2 " model vdw 2.249 3.040 nonbonded pdb=" O4 NAG S 2 " pdb=" O6 NAG S 2 " model vdw 2.249 3.040 ... (remaining 162982 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'R' selection = chain 'e' selection = chain 'r' } ncs_group { reference = chain 'W' selection = chain 'j' selection = chain 'w' } 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: 1.100 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.510 Find NCS groups from input model: 0.630 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.020 0.116 21003 Z= 1.051 Angle : 1.826 11.971 28770 Z= 1.158 Chirality : 0.102 0.324 3516 Planarity : 0.009 0.081 3465 Dihedral : 12.879 109.747 9357 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.34 % Rotamer: Outliers : 0.72 % Allowed : 0.58 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.59 (0.17), residues: 2364 helix: -0.50 (0.25), residues: 381 sheet: 1.10 (0.19), residues: 675 loop : 0.42 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 50 TYR 0.078 0.008 TYR L 36 PHE 0.038 0.007 PHE A 383 TRP 0.057 0.011 TRP I 610 HIS 0.019 0.003 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.01915 (20853) covalent geometry : angle 1.80525 (28353) SS BOND : bond 0.03128 ( 33) SS BOND : angle 2.57998 ( 66) hydrogen bonds : bond 0.17058 ( 720) hydrogen bonds : angle 7.32289 ( 1980) link_ALPHA1-3 : bond 0.06587 ( 3) link_ALPHA1-3 : angle 2.80760 ( 9) link_BETA1-4 : bond 0.06175 ( 45) link_BETA1-4 : angle 3.19742 ( 135) link_NAG-ASN : bond 0.05096 ( 69) link_NAG-ASN : angle 2.83342 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 680 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8197 (t0) cc_final: 0.7744 (t0) REVERT: A 256 SER cc_start: 0.8648 (p) cc_final: 0.8381 (p) REVERT: A 279 ASP cc_start: 0.8479 (t0) cc_final: 0.8219 (t0) REVERT: A 317 PHE cc_start: 0.8782 (t80) cc_final: 0.8524 (t80) REVERT: A 439 ILE cc_start: 0.8866 (pt) cc_final: 0.8549 (mm) REVERT: B 542 ARG cc_start: 0.6467 (mtp180) cc_final: 0.5938 (mmt180) REVERT: B 639 THR cc_start: 0.9018 (m) cc_final: 0.8708 (p) REVERT: L 77 ASP cc_start: 0.8015 (t0) cc_final: 0.7337 (t0) REVERT: H 59 TYR cc_start: 0.7810 (m-80) cc_final: 0.7584 (m-80) REVERT: H 79 LEU cc_start: 0.8005 (tp) cc_final: 0.7205 (tp) REVERT: H 82 LEU cc_start: 0.9304 (mt) cc_final: 0.8805 (mt) REVERT: C 78 ASP cc_start: 0.8173 (t0) cc_final: 0.7777 (t0) REVERT: C 107 ASP cc_start: 0.8628 (m-30) cc_final: 0.8186 (m-30) REVERT: C 279 ASP cc_start: 0.8656 (t0) cc_final: 0.8245 (t0) REVERT: C 439 ILE cc_start: 0.9031 (pt) cc_final: 0.8738 (mm) REVERT: D 542 ARG cc_start: 0.6625 (mtp180) cc_final: 0.6072 (mmt180) REVERT: D 639 THR cc_start: 0.9000 (m) cc_final: 0.8653 (p) REVERT: E 77 ASP cc_start: 0.7885 (t0) cc_final: 0.7657 (t0) REVERT: E 95 ASP cc_start: 0.7415 (m-30) cc_final: 0.7173 (m-30) REVERT: F 39 GLN cc_start: 0.8104 (tt0) cc_final: 0.7443 (tm-30) REVERT: F 82 LEU cc_start: 0.9260 (mt) cc_final: 0.8608 (mt) REVERT: G 439 ILE cc_start: 0.8801 (pt) cc_final: 0.8498 (mm) REVERT: I 542 ARG cc_start: 0.6202 (mtp180) cc_final: 0.5839 (mmt180) REVERT: I 627 THR cc_start: 0.8920 (m) cc_final: 0.7958 (p) REVERT: I 639 THR cc_start: 0.9011 (m) cc_final: 0.8437 (p) REVERT: J 77 ASP cc_start: 0.7917 (t0) cc_final: 0.7663 (t0) REVERT: K 39 GLN cc_start: 0.8331 (tt0) cc_final: 0.7734 (tm-30) REVERT: K 82 LEU cc_start: 0.9231 (mt) cc_final: 0.8668 (mt) outliers start: 15 outliers final: 6 residues processed: 692 average time/residue: 0.1580 time to fit residues: 166.3652 Evaluate side-chains 365 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 359 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain I residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.0070 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 607 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN F 35 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 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 = 0.3541 r_free = 0.3541 target = 0.094688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072253 restraints weight = 52051.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075722 restraints weight = 25463.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078087 restraints weight = 16402.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079709 restraints weight = 12339.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080825 restraints weight = 10172.137| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21003 Z= 0.182 Angle : 0.866 9.949 28770 Z= 0.434 Chirality : 0.048 0.212 3516 Planarity : 0.005 0.042 3465 Dihedral : 9.207 69.031 5031 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.84 % Allowed : 12.38 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: 0.27 (0.17), residues: 2364 helix: 0.56 (0.26), residues: 378 sheet: 0.65 (0.18), residues: 684 loop : -0.12 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 66 TYR 0.022 0.002 TYR K 100C PHE 0.020 0.003 PHE A 391 TRP 0.038 0.003 TRP H 36 HIS 0.004 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00397 (20853) covalent geometry : angle 0.82634 (28353) SS BOND : bond 0.00249 ( 33) SS BOND : angle 1.20834 ( 66) hydrogen bonds : bond 0.06015 ( 720) hydrogen bonds : angle 6.04645 ( 1980) link_ALPHA1-3 : bond 0.00979 ( 3) link_ALPHA1-3 : angle 1.97439 ( 9) link_BETA1-4 : bond 0.00706 ( 45) link_BETA1-4 : angle 2.10787 ( 135) link_NAG-ASN : bond 0.00576 ( 69) link_NAG-ASN : angle 2.69120 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 478 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8352 (ptm) cc_final: 0.8060 (ptp) REVERT: A 117 LYS cc_start: 0.8944 (tttt) cc_final: 0.8695 (ttmm) REVERT: A 302 ASN cc_start: 0.7915 (t0) cc_final: 0.7714 (t0) REVERT: A 370 GLU cc_start: 0.8192 (tp30) cc_final: 0.7902 (tp30) REVERT: B 530 MET cc_start: 0.7457 (mmm) cc_final: 0.6769 (mmm) REVERT: B 566 LEU cc_start: 0.8398 (tt) cc_final: 0.8179 (tt) REVERT: B 621 GLU cc_start: 0.8286 (tt0) cc_final: 0.7946 (tt0) REVERT: B 639 THR cc_start: 0.8997 (m) cc_final: 0.8785 (p) REVERT: B 647 GLU cc_start: 0.9278 (tt0) cc_final: 0.9069 (tt0) REVERT: L 21 ILE cc_start: 0.9030 (mm) cc_final: 0.8467 (tp) REVERT: L 42 GLN cc_start: 0.7140 (mp10) cc_final: 0.6569 (mp10) REVERT: L 77 ASP cc_start: 0.8011 (t0) cc_final: 0.7090 (t0) REVERT: L 78 LEU cc_start: 0.8548 (mp) cc_final: 0.8260 (mp) REVERT: L 95 ASP cc_start: 0.7270 (m-30) cc_final: 0.6714 (m-30) REVERT: H 7 SER cc_start: 0.8413 (p) cc_final: 0.8110 (p) REVERT: H 30 SER cc_start: 0.9271 (m) cc_final: 0.8964 (m) REVERT: H 33 HIS cc_start: 0.8501 (m170) cc_final: 0.8220 (m170) REVERT: H 36 TRP cc_start: 0.8325 (m100) cc_final: 0.7850 (m-10) REVERT: H 57 ILE cc_start: 0.9439 (pt) cc_final: 0.9126 (mp) REVERT: H 79 LEU cc_start: 0.8553 (tp) cc_final: 0.8303 (tp) REVERT: C 67 ASN cc_start: 0.8753 (m-40) cc_final: 0.8552 (t0) REVERT: C 370 GLU cc_start: 0.8341 (tp30) cc_final: 0.8118 (tp30) REVERT: C 424 ILE cc_start: 0.9425 (pp) cc_final: 0.9224 (pp) REVERT: D 566 LEU cc_start: 0.8799 (tp) cc_final: 0.8328 (tt) REVERT: D 595 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 603 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8429 (pt) REVERT: D 627 THR cc_start: 0.8394 (p) cc_final: 0.8159 (t) REVERT: D 630 GLN cc_start: 0.8886 (mt0) cc_final: 0.8348 (mt0) REVERT: D 647 GLU cc_start: 0.9067 (tt0) cc_final: 0.8696 (tp30) REVERT: D 653 GLN cc_start: 0.8995 (tt0) cc_final: 0.8697 (pp30) REVERT: E 42 GLN cc_start: 0.7476 (mp10) cc_final: 0.6843 (mp10) REVERT: E 77 ASP cc_start: 0.8157 (t0) cc_final: 0.7019 (t0) REVERT: E 78 LEU cc_start: 0.8744 (mp) cc_final: 0.8406 (mp) REVERT: E 95 ASP cc_start: 0.7605 (m-30) cc_final: 0.7206 (m-30) REVERT: F 7 SER cc_start: 0.8194 (p) cc_final: 0.7956 (p) REVERT: F 30 SER cc_start: 0.9297 (m) cc_final: 0.8876 (m) REVERT: F 33 HIS cc_start: 0.8508 (m170) cc_final: 0.8176 (m170) REVERT: F 57 ILE cc_start: 0.9480 (pt) cc_final: 0.9182 (mp) REVERT: F 59 TYR cc_start: 0.7743 (m-80) cc_final: 0.7330 (m-80) REVERT: F 62 TRP cc_start: 0.8689 (t-100) cc_final: 0.8141 (t-100) REVERT: G 67 ASN cc_start: 0.8649 (m-40) cc_final: 0.8240 (t0) REVERT: G 74 CYS cc_start: 0.8017 (m) cc_final: 0.7427 (m) REVERT: G 195 ASN cc_start: 0.7926 (m-40) cc_final: 0.7565 (m-40) REVERT: G 251 ILE cc_start: 0.8012 (mt) cc_final: 0.7804 (pt) REVERT: G 370 GLU cc_start: 0.8384 (tp30) cc_final: 0.8125 (tp30) REVERT: G 398 THR cc_start: 0.8330 (p) cc_final: 0.7797 (t) REVERT: I 530 MET cc_start: 0.7287 (mmm) cc_final: 0.6551 (mmm) REVERT: I 566 LEU cc_start: 0.8436 (tp) cc_final: 0.7971 (tt) REVERT: I 622 ILE cc_start: 0.8678 (mt) cc_final: 0.8338 (mp) REVERT: J 42 GLN cc_start: 0.7252 (mp10) cc_final: 0.6753 (mp10) REVERT: J 63 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8359 (mmtt) REVERT: J 77 ASP cc_start: 0.7989 (t0) cc_final: 0.7244 (t0) REVERT: J 78 LEU cc_start: 0.8462 (mp) cc_final: 0.8177 (mp) REVERT: J 95 ASP cc_start: 0.7659 (m-30) cc_final: 0.7163 (m-30) REVERT: K 7 SER cc_start: 0.8456 (p) cc_final: 0.8087 (p) REVERT: K 30 SER cc_start: 0.9246 (m) cc_final: 0.8847 (m) REVERT: K 33 HIS cc_start: 0.8633 (m170) cc_final: 0.8321 (m170) REVERT: K 57 ILE cc_start: 0.9371 (pt) cc_final: 0.9058 (mp) REVERT: K 58 TYR cc_start: 0.7760 (p90) cc_final: 0.7537 (p90) REVERT: K 59 TYR cc_start: 0.7676 (m-80) cc_final: 0.7214 (m-80) REVERT: K 62 TRP cc_start: 0.8618 (t-100) cc_final: 0.8095 (t-100) outliers start: 59 outliers final: 34 residues processed: 511 average time/residue: 0.1440 time to fit residues: 116.7664 Evaluate side-chains 397 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 361 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 202 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 422 GLN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 330 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 203 GLN G 330 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.066621 restraints weight = 53614.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069781 restraints weight = 27030.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071976 restraints weight = 17870.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.073444 restraints weight = 13660.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074430 restraints weight = 11451.250| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21003 Z= 0.237 Angle : 0.826 17.029 28770 Z= 0.405 Chirality : 0.049 0.230 3516 Planarity : 0.004 0.054 3465 Dihedral : 7.339 56.685 5025 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.43 % Allowed : 14.31 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.18 (0.17), residues: 2364 helix: 0.54 (0.27), residues: 372 sheet: 0.51 (0.19), residues: 666 loop : -0.61 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 28 TYR 0.021 0.002 TYR H 100C PHE 0.037 0.003 PHE L 96 TRP 0.036 0.002 TRP A 479 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00539 (20853) covalent geometry : angle 0.79028 (28353) SS BOND : bond 0.00291 ( 33) SS BOND : angle 1.01372 ( 66) hydrogen bonds : bond 0.05420 ( 720) hydrogen bonds : angle 5.71093 ( 1980) link_ALPHA1-3 : bond 0.01011 ( 3) link_ALPHA1-3 : angle 2.13461 ( 9) link_BETA1-4 : bond 0.00722 ( 45) link_BETA1-4 : angle 1.82544 ( 135) link_NAG-ASN : bond 0.00513 ( 69) link_NAG-ASN : angle 2.56614 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 386 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8355 (ptm) cc_final: 0.8057 (ptp) REVERT: A 180 ASP cc_start: 0.8920 (m-30) cc_final: 0.8676 (t0) REVERT: A 420 ILE cc_start: 0.9266 (mp) cc_final: 0.8899 (mt) REVERT: B 530 MET cc_start: 0.7609 (mmm) cc_final: 0.7010 (mmm) REVERT: B 621 GLU cc_start: 0.8888 (tt0) cc_final: 0.8530 (tt0) REVERT: B 626 MET cc_start: 0.8083 (tpp) cc_final: 0.7841 (tpp) REVERT: B 629 MET cc_start: 0.8716 (mmt) cc_final: 0.8450 (tpp) REVERT: L 21 ILE cc_start: 0.9027 (mm) cc_final: 0.8472 (tp) REVERT: L 42 GLN cc_start: 0.7047 (mp10) cc_final: 0.6618 (mp10) REVERT: L 61 ARG cc_start: 0.8590 (ptp-170) cc_final: 0.7982 (mpp80) REVERT: L 75 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8755 (tp) REVERT: L 77 ASP cc_start: 0.7717 (t0) cc_final: 0.7320 (t0) REVERT: L 82 ASP cc_start: 0.6462 (p0) cc_final: 0.6004 (p0) REVERT: L 95 ASP cc_start: 0.7413 (m-30) cc_final: 0.6908 (p0) REVERT: H 13 GLN cc_start: 0.8700 (pp30) cc_final: 0.8456 (pp30) REVERT: H 15 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8544 (tp30) REVERT: H 20 LEU cc_start: 0.9434 (mm) cc_final: 0.9023 (mm) REVERT: H 31 ASP cc_start: 0.8999 (p0) cc_final: 0.8707 (p0) REVERT: H 33 HIS cc_start: 0.8853 (m170) cc_final: 0.8407 (m170) REVERT: H 57 ILE cc_start: 0.9554 (pt) cc_final: 0.9246 (mp) REVERT: C 67 ASN cc_start: 0.8921 (m-40) cc_final: 0.8628 (t0) REVERT: C 370 GLU cc_start: 0.8398 (tp30) cc_final: 0.8068 (tp30) REVERT: C 398 THR cc_start: 0.8331 (p) cc_final: 0.8009 (t) REVERT: C 420 ILE cc_start: 0.9182 (mp) cc_final: 0.8790 (mt) REVERT: D 566 LEU cc_start: 0.8931 (tp) cc_final: 0.8480 (tt) REVERT: D 595 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8874 (tp) REVERT: D 652 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8523 (mp10) REVERT: D 653 GLN cc_start: 0.9049 (tt0) cc_final: 0.8409 (tm-30) REVERT: E 4 MET cc_start: 0.6859 (mmm) cc_final: 0.5734 (tpp) REVERT: E 24 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8214 (mm110) REVERT: E 36 TYR cc_start: 0.7324 (m-80) cc_final: 0.6759 (m-80) REVERT: E 42 GLN cc_start: 0.7412 (mp10) cc_final: 0.6859 (mp10) REVERT: E 63 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8135 (mmtt) REVERT: E 75 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8728 (tp) REVERT: E 77 ASP cc_start: 0.7760 (t0) cc_final: 0.7306 (t0) REVERT: E 82 ASP cc_start: 0.6481 (p0) cc_final: 0.6159 (p0) REVERT: E 95 ASP cc_start: 0.7812 (m-30) cc_final: 0.7313 (p0) REVERT: F 36 TRP cc_start: 0.8302 (m100) cc_final: 0.7789 (m100) REVERT: F 57 ILE cc_start: 0.9571 (pt) cc_final: 0.9229 (mp) REVERT: F 59 TYR cc_start: 0.8076 (m-80) cc_final: 0.7702 (m-80) REVERT: F 62 TRP cc_start: 0.8675 (t-100) cc_final: 0.8474 (t-100) REVERT: G 67 ASN cc_start: 0.8806 (m-40) cc_final: 0.8408 (t0) REVERT: G 74 CYS cc_start: 0.8203 (m) cc_final: 0.7621 (m) REVERT: G 95 MET cc_start: 0.7609 (ptp) cc_final: 0.7211 (ptp) REVERT: G 122 LEU cc_start: 0.9096 (mp) cc_final: 0.8807 (tt) REVERT: G 398 THR cc_start: 0.8522 (p) cc_final: 0.8192 (t) REVERT: G 420 ILE cc_start: 0.9250 (mp) cc_final: 0.8886 (mt) REVERT: G 434 MET cc_start: 0.8528 (ttm) cc_final: 0.8263 (ttm) REVERT: I 530 MET cc_start: 0.7699 (mmm) cc_final: 0.6946 (mmm) REVERT: I 595 ILE cc_start: 0.9234 (tp) cc_final: 0.8714 (tt) REVERT: I 621 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8095 (tm-30) REVERT: I 622 ILE cc_start: 0.8910 (mt) cc_final: 0.8387 (mp) REVERT: I 634 GLU cc_start: 0.8647 (tt0) cc_final: 0.8276 (tm-30) REVERT: I 653 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: J 6 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6742 (mp10) REVERT: J 42 GLN cc_start: 0.7082 (mp10) cc_final: 0.6660 (mp10) REVERT: J 63 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8356 (mmtt) REVERT: J 75 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8769 (tp) REVERT: J 77 ASP cc_start: 0.8200 (t0) cc_final: 0.7941 (t0) REVERT: J 82 ASP cc_start: 0.6566 (p0) cc_final: 0.6238 (p0) REVERT: J 95 ASP cc_start: 0.7816 (m-30) cc_final: 0.6984 (p0) REVERT: K 6 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: K 31 ASP cc_start: 0.9089 (p0) cc_final: 0.8848 (p0) REVERT: K 33 HIS cc_start: 0.8889 (m170) cc_final: 0.8574 (m170) REVERT: K 38 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7645 (ttm170) REVERT: K 59 TYR cc_start: 0.8022 (m-80) cc_final: 0.7338 (m-80) outliers start: 92 outliers final: 46 residues processed: 444 average time/residue: 0.1384 time to fit residues: 98.5128 Evaluate side-chains 383 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 330 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 653 GLN Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 67 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN H 35 GLN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN K 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.091045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.068680 restraints weight = 53235.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071955 restraints weight = 26671.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074190 restraints weight = 17455.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075707 restraints weight = 13292.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.076719 restraints weight = 11077.044| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21003 Z= 0.143 Angle : 0.734 15.170 28770 Z= 0.356 Chirality : 0.046 0.228 3516 Planarity : 0.004 0.045 3465 Dihedral : 6.218 41.072 5025 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.23 % Allowed : 14.84 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.14 (0.17), residues: 2364 helix: 0.74 (0.27), residues: 363 sheet: 0.43 (0.19), residues: 726 loop : -0.61 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 469 TYR 0.016 0.001 TYR K 58 PHE 0.020 0.002 PHE L 96 TRP 0.053 0.002 TRP H 36 HIS 0.009 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00317 (20853) covalent geometry : angle 0.70020 (28353) SS BOND : bond 0.00157 ( 33) SS BOND : angle 0.66245 ( 66) hydrogen bonds : bond 0.04717 ( 720) hydrogen bonds : angle 5.50452 ( 1980) link_ALPHA1-3 : bond 0.00977 ( 3) link_ALPHA1-3 : angle 2.56577 ( 9) link_BETA1-4 : bond 0.00647 ( 45) link_BETA1-4 : angle 1.53410 ( 135) link_NAG-ASN : bond 0.00392 ( 69) link_NAG-ASN : angle 2.40778 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 376 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8623 (tt) cc_final: 0.8373 (tt) REVERT: A 180 ASP cc_start: 0.9028 (m-30) cc_final: 0.8729 (t0) REVERT: A 420 ILE cc_start: 0.9209 (mp) cc_final: 0.8872 (mt) REVERT: B 530 MET cc_start: 0.7759 (mmm) cc_final: 0.7144 (mmm) REVERT: B 595 ILE cc_start: 0.9029 (tp) cc_final: 0.8454 (tt) REVERT: B 621 GLU cc_start: 0.8959 (tt0) cc_final: 0.8588 (tt0) REVERT: B 626 MET cc_start: 0.8099 (tpp) cc_final: 0.7656 (ttt) REVERT: B 647 GLU cc_start: 0.9151 (tt0) cc_final: 0.8859 (tt0) REVERT: L 21 ILE cc_start: 0.8825 (mm) cc_final: 0.8376 (tp) REVERT: L 42 GLN cc_start: 0.6964 (mp10) cc_final: 0.6629 (mp10) REVERT: L 61 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.7944 (mpp80) REVERT: L 75 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8681 (tp) REVERT: L 77 ASP cc_start: 0.7568 (t0) cc_final: 0.7075 (t0) REVERT: L 82 ASP cc_start: 0.6118 (p0) cc_final: 0.5518 (p0) REVERT: L 95 ASP cc_start: 0.7375 (m-30) cc_final: 0.6869 (p0) REVERT: H 5 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7963 (tm-30) REVERT: H 13 GLN cc_start: 0.8793 (pp30) cc_final: 0.8470 (pp30) REVERT: H 15 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8437 (tp30) REVERT: H 30 SER cc_start: 0.9285 (m) cc_final: 0.9070 (m) REVERT: H 33 HIS cc_start: 0.8787 (m170) cc_final: 0.8446 (m170) REVERT: H 57 ILE cc_start: 0.9585 (pt) cc_final: 0.9340 (mp) REVERT: H 100 TYR cc_start: 0.8421 (p90) cc_final: 0.8110 (p90) REVERT: C 67 ASN cc_start: 0.8816 (m-40) cc_final: 0.8556 (t0) REVERT: C 268 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7181 (mt-10) REVERT: C 420 ILE cc_start: 0.9151 (mp) cc_final: 0.8789 (mt) REVERT: D 566 LEU cc_start: 0.8948 (tp) cc_final: 0.8527 (tt) REVERT: D 595 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8738 (tp) REVERT: D 621 GLU cc_start: 0.9002 (tt0) cc_final: 0.7990 (tm-30) REVERT: D 622 ILE cc_start: 0.8749 (mt) cc_final: 0.7874 (mt) REVERT: D 647 GLU cc_start: 0.9078 (tt0) cc_final: 0.8816 (tp30) REVERT: E 4 MET cc_start: 0.6943 (mmm) cc_final: 0.6173 (tpp) REVERT: E 24 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8259 (mm-40) REVERT: E 36 TYR cc_start: 0.7280 (m-80) cc_final: 0.6733 (m-80) REVERT: E 42 GLN cc_start: 0.7314 (mp10) cc_final: 0.6874 (mp10) REVERT: E 75 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8668 (tp) REVERT: E 77 ASP cc_start: 0.7608 (t0) cc_final: 0.7082 (t0) REVERT: E 82 ASP cc_start: 0.6063 (p0) cc_final: 0.5597 (p0) REVERT: E 95 ASP cc_start: 0.7834 (m-30) cc_final: 0.7405 (p0) REVERT: F 5 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8210 (tm-30) REVERT: F 28 ASP cc_start: 0.6872 (t0) cc_final: 0.6617 (t0) REVERT: F 30 SER cc_start: 0.9057 (m) cc_final: 0.8738 (m) REVERT: F 31 ASP cc_start: 0.9082 (p0) cc_final: 0.8787 (p0) REVERT: F 33 HIS cc_start: 0.8940 (m170) cc_final: 0.8721 (m-70) REVERT: F 57 ILE cc_start: 0.9577 (pt) cc_final: 0.9274 (mp) REVERT: F 59 TYR cc_start: 0.8136 (m-80) cc_final: 0.7766 (m-80) REVERT: F 100 TYR cc_start: 0.8271 (p90) cc_final: 0.7907 (p90) REVERT: G 67 ASN cc_start: 0.8750 (m-40) cc_final: 0.8348 (t0) REVERT: G 74 CYS cc_start: 0.8127 (m) cc_final: 0.7527 (m) REVERT: G 95 MET cc_start: 0.7489 (ptp) cc_final: 0.7084 (ptp) REVERT: G 122 LEU cc_start: 0.8983 (mp) cc_final: 0.8766 (tp) REVERT: G 398 THR cc_start: 0.8611 (p) cc_final: 0.8315 (t) REVERT: G 420 ILE cc_start: 0.9176 (mp) cc_final: 0.8839 (mt) REVERT: G 434 MET cc_start: 0.8488 (ttm) cc_final: 0.8119 (ttm) REVERT: I 530 MET cc_start: 0.7491 (mmm) cc_final: 0.6687 (mmm) REVERT: I 566 LEU cc_start: 0.8483 (tp) cc_final: 0.8248 (tt) REVERT: I 595 ILE cc_start: 0.9107 (tp) cc_final: 0.8681 (tp) REVERT: I 629 MET cc_start: 0.8669 (mmm) cc_final: 0.8142 (mmm) REVERT: I 634 GLU cc_start: 0.8679 (tt0) cc_final: 0.8339 (tm-30) REVERT: I 647 GLU cc_start: 0.9055 (tt0) cc_final: 0.8632 (tp30) REVERT: J 21 ILE cc_start: 0.8759 (mm) cc_final: 0.8342 (tp) REVERT: J 42 GLN cc_start: 0.7035 (mp10) cc_final: 0.6650 (mp10) REVERT: J 77 ASP cc_start: 0.7916 (t0) cc_final: 0.7677 (t0) REVERT: J 82 ASP cc_start: 0.5929 (p0) cc_final: 0.5575 (p0) REVERT: J 95 ASP cc_start: 0.7654 (m-30) cc_final: 0.6908 (p0) REVERT: K 5 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7874 (tm-30) REVERT: K 6 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6028 (mp0) REVERT: K 28 ASP cc_start: 0.7089 (t0) cc_final: 0.6831 (t0) REVERT: K 30 SER cc_start: 0.9113 (m) cc_final: 0.8886 (m) REVERT: K 31 ASP cc_start: 0.9161 (p0) cc_final: 0.8935 (p0) REVERT: K 33 HIS cc_start: 0.8810 (m170) cc_final: 0.8541 (m170) REVERT: K 47 PHE cc_start: 0.8001 (t80) cc_final: 0.7521 (t80) REVERT: K 57 ILE cc_start: 0.9554 (pt) cc_final: 0.9175 (mp) REVERT: K 58 TYR cc_start: 0.7779 (p90) cc_final: 0.7218 (p90) REVERT: K 59 TYR cc_start: 0.8153 (m-80) cc_final: 0.7579 (m-80) REVERT: K 100 TYR cc_start: 0.8280 (p90) cc_final: 0.7916 (p90) outliers start: 67 outliers final: 44 residues processed: 419 average time/residue: 0.1370 time to fit residues: 92.1276 Evaluate side-chains 383 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 87 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN L 27 GLN H 35 GLN C 203 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** K 35 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 = 0.3409 r_free = 0.3409 target = 0.087695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.065354 restraints weight = 54379.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.068416 restraints weight = 27649.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070530 restraints weight = 18377.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071934 restraints weight = 14102.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072896 restraints weight = 11864.841| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21003 Z= 0.219 Angle : 0.766 15.496 28770 Z= 0.370 Chirality : 0.047 0.220 3516 Planarity : 0.004 0.042 3465 Dihedral : 6.068 35.102 5019 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.85 % Allowed : 15.41 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.35 (0.17), residues: 2364 helix: 0.68 (0.28), residues: 366 sheet: 0.33 (0.19), residues: 729 loop : -0.83 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.019 0.002 TYR E 49 PHE 0.027 0.003 PHE L 96 TRP 0.053 0.002 TRP H 36 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00503 (20853) covalent geometry : angle 0.73373 (28353) SS BOND : bond 0.00246 ( 33) SS BOND : angle 0.73205 ( 66) hydrogen bonds : bond 0.04904 ( 720) hydrogen bonds : angle 5.50144 ( 1980) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 2.13479 ( 9) link_BETA1-4 : bond 0.00595 ( 45) link_BETA1-4 : angle 1.59169 ( 135) link_NAG-ASN : bond 0.00508 ( 69) link_NAG-ASN : angle 2.41252 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 352 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8730 (p) cc_final: 0.8465 (p) REVERT: A 420 ILE cc_start: 0.9273 (mp) cc_final: 0.8957 (mt) REVERT: B 530 MET cc_start: 0.7755 (mmm) cc_final: 0.7290 (mmm) REVERT: B 621 GLU cc_start: 0.8958 (tt0) cc_final: 0.8576 (tt0) REVERT: B 626 MET cc_start: 0.8386 (tpp) cc_final: 0.7897 (ttt) REVERT: B 647 GLU cc_start: 0.9084 (tt0) cc_final: 0.8814 (tp30) REVERT: L 4 MET cc_start: 0.6842 (mmm) cc_final: 0.6186 (tpp) REVERT: L 21 ILE cc_start: 0.8770 (mm) cc_final: 0.8341 (tp) REVERT: L 27 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: L 42 GLN cc_start: 0.7001 (mp10) cc_final: 0.6627 (mp10) REVERT: L 75 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8719 (tp) REVERT: L 77 ASP cc_start: 0.7688 (t0) cc_final: 0.7217 (t0) REVERT: L 82 ASP cc_start: 0.6056 (p0) cc_final: 0.5528 (p0) REVERT: L 95 ASP cc_start: 0.7512 (m-30) cc_final: 0.7230 (m-30) REVERT: H 15 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8455 (tp30) REVERT: H 31 ASP cc_start: 0.9033 (p0) cc_final: 0.8742 (p0) REVERT: H 33 HIS cc_start: 0.9014 (m170) cc_final: 0.8512 (m170) REVERT: H 57 ILE cc_start: 0.9582 (pt) cc_final: 0.9353 (mp) REVERT: H 59 TYR cc_start: 0.8052 (m-80) cc_final: 0.7424 (m-80) REVERT: C 67 ASN cc_start: 0.8907 (m-40) cc_final: 0.8621 (t0) REVERT: C 116 LEU cc_start: 0.8343 (tt) cc_final: 0.8065 (tt) REVERT: C 420 ILE cc_start: 0.9235 (mp) cc_final: 0.8900 (mt) REVERT: D 566 LEU cc_start: 0.9035 (tp) cc_final: 0.8591 (tt) REVERT: D 595 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8831 (tp) REVERT: D 602 ILE cc_start: 0.9199 (mm) cc_final: 0.8704 (tp) REVERT: D 621 GLU cc_start: 0.9068 (tt0) cc_final: 0.8778 (tt0) REVERT: D 647 GLU cc_start: 0.9046 (tt0) cc_final: 0.8811 (tp30) REVERT: E 36 TYR cc_start: 0.7428 (m-80) cc_final: 0.6905 (m-80) REVERT: E 42 GLN cc_start: 0.7232 (mp10) cc_final: 0.6781 (mp10) REVERT: E 75 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8625 (tp) REVERT: E 77 ASP cc_start: 0.7707 (t0) cc_final: 0.7234 (t0) REVERT: E 82 ASP cc_start: 0.6258 (p0) cc_final: 0.5751 (p0) REVERT: E 95 ASP cc_start: 0.7876 (m-30) cc_final: 0.7565 (m-30) REVERT: F 4 LEU cc_start: 0.6091 (mm) cc_final: 0.5888 (mm) REVERT: F 28 ASP cc_start: 0.6933 (t0) cc_final: 0.6620 (t0) REVERT: F 30 SER cc_start: 0.9162 (m) cc_final: 0.8806 (m) REVERT: F 31 ASP cc_start: 0.9158 (p0) cc_final: 0.8786 (p0) REVERT: F 36 TRP cc_start: 0.8591 (m100) cc_final: 0.8174 (m-10) REVERT: F 57 ILE cc_start: 0.9578 (pt) cc_final: 0.9283 (mp) REVERT: F 59 TYR cc_start: 0.8312 (m-80) cc_final: 0.8109 (m-80) REVERT: F 100 TYR cc_start: 0.8672 (p90) cc_final: 0.8333 (p90) REVERT: G 67 ASN cc_start: 0.8800 (m-40) cc_final: 0.8377 (t0) REVERT: G 74 CYS cc_start: 0.8129 (m) cc_final: 0.7522 (m) REVERT: G 95 MET cc_start: 0.7615 (ptp) cc_final: 0.7234 (ptp) REVERT: G 122 LEU cc_start: 0.9109 (mp) cc_final: 0.8867 (tt) REVERT: G 180 ASP cc_start: 0.9148 (m-30) cc_final: 0.8945 (t0) REVERT: G 398 THR cc_start: 0.8681 (p) cc_final: 0.8407 (t) REVERT: G 420 ILE cc_start: 0.9319 (mp) cc_final: 0.9041 (mt) REVERT: G 434 MET cc_start: 0.8602 (ttm) cc_final: 0.8135 (ttm) REVERT: I 529 THR cc_start: 0.8304 (m) cc_final: 0.8048 (m) REVERT: I 530 MET cc_start: 0.7667 (mmm) cc_final: 0.7098 (mmm) REVERT: I 629 MET cc_start: 0.8779 (mmm) cc_final: 0.8324 (mmm) REVERT: I 647 GLU cc_start: 0.9038 (tt0) cc_final: 0.8693 (tp30) REVERT: J 21 ILE cc_start: 0.8628 (mm) cc_final: 0.8295 (tp) REVERT: J 42 GLN cc_start: 0.6744 (mp10) cc_final: 0.6382 (mp10) REVERT: J 63 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8321 (mmtt) REVERT: J 75 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8628 (tp) REVERT: J 77 ASP cc_start: 0.8026 (t0) cc_final: 0.7703 (t0) REVERT: J 82 ASP cc_start: 0.6177 (p0) cc_final: 0.5622 (p0) REVERT: K 6 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: K 28 ASP cc_start: 0.7241 (t0) cc_final: 0.6950 (t0) REVERT: K 30 SER cc_start: 0.9109 (m) cc_final: 0.8785 (m) REVERT: K 31 ASP cc_start: 0.9203 (p0) cc_final: 0.8980 (p0) REVERT: K 33 HIS cc_start: 0.8988 (m170) cc_final: 0.8611 (m170) REVERT: K 38 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7688 (ttm-80) REVERT: K 57 ILE cc_start: 0.9576 (pt) cc_final: 0.9175 (mp) REVERT: K 59 TYR cc_start: 0.8223 (m-80) cc_final: 0.7690 (m-80) outliers start: 80 outliers final: 59 residues processed: 395 average time/residue: 0.1435 time to fit residues: 89.8511 Evaluate side-chains 392 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 326 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 38 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 161 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 162 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 27 GLN H 35 GLN E 70 GLN ** I 650 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 = 0.3450 r_free = 0.3450 target = 0.092573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072395 restraints weight = 52267.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075075 restraints weight = 30580.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076908 restraints weight = 21636.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078081 restraints weight = 17224.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078929 restraints weight = 14838.546| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21003 Z= 0.138 Angle : 0.705 15.617 28770 Z= 0.342 Chirality : 0.046 0.272 3516 Planarity : 0.004 0.064 3465 Dihedral : 5.622 32.692 5019 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.42 % Allowed : 16.47 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.34 (0.17), residues: 2364 helix: 0.70 (0.27), residues: 366 sheet: 0.38 (0.19), residues: 729 loop : -0.85 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.021 0.001 TYR F 58 PHE 0.027 0.002 PHE L 96 TRP 0.050 0.002 TRP H 36 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00310 (20853) covalent geometry : angle 0.67514 (28353) SS BOND : bond 0.00155 ( 33) SS BOND : angle 0.59493 ( 66) hydrogen bonds : bond 0.04460 ( 720) hydrogen bonds : angle 5.35779 ( 1980) link_ALPHA1-3 : bond 0.00985 ( 3) link_ALPHA1-3 : angle 2.10179 ( 9) link_BETA1-4 : bond 0.00600 ( 45) link_BETA1-4 : angle 1.48231 ( 135) link_NAG-ASN : bond 0.00382 ( 69) link_NAG-ASN : angle 2.23059 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 364 time to evaluate : 0.739 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 373 THR cc_start: 0.8514 (p) cc_final: 0.8247 (p) REVERT: A 420 ILE cc_start: 0.9134 (mp) cc_final: 0.8800 (mt) REVERT: A 479 TRP cc_start: 0.8409 (m-10) cc_final: 0.8061 (m-90) REVERT: B 530 MET cc_start: 0.7199 (mmm) cc_final: 0.6911 (mmm) REVERT: B 621 GLU cc_start: 0.8592 (tt0) cc_final: 0.8254 (tt0) REVERT: L 42 GLN cc_start: 0.7364 (mp10) cc_final: 0.6908 (mp10) REVERT: L 75 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8483 (tp) REVERT: L 82 ASP cc_start: 0.5975 (p0) cc_final: 0.5603 (p0) REVERT: L 95 ASP cc_start: 0.7402 (m-30) cc_final: 0.7052 (m-30) REVERT: H 13 GLN cc_start: 0.8456 (pp30) cc_final: 0.8249 (pp30) REVERT: H 15 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8244 (tp30) REVERT: H 28 ASP cc_start: 0.7569 (t0) cc_final: 0.7349 (t0) REVERT: H 30 SER cc_start: 0.9261 (m) cc_final: 0.9008 (m) REVERT: C 74 CYS cc_start: 0.7700 (m) cc_final: 0.7461 (m) REVERT: C 420 ILE cc_start: 0.9154 (mp) cc_final: 0.8835 (mt) REVERT: D 595 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9110 (tp) REVERT: D 602 ILE cc_start: 0.9476 (mm) cc_final: 0.9097 (tp) REVERT: D 621 GLU cc_start: 0.8779 (tt0) cc_final: 0.8430 (tt0) REVERT: E 42 GLN cc_start: 0.7661 (mp10) cc_final: 0.7262 (mp10) REVERT: E 77 ASP cc_start: 0.7419 (t0) cc_final: 0.7214 (t0) REVERT: E 82 ASP cc_start: 0.5923 (p0) cc_final: 0.5611 (p0) REVERT: F 28 ASP cc_start: 0.6974 (t0) cc_final: 0.6537 (t0) REVERT: F 30 SER cc_start: 0.9086 (m) cc_final: 0.8748 (m) REVERT: F 31 ASP cc_start: 0.8754 (p0) cc_final: 0.8441 (p0) REVERT: F 38 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7804 (ttm170) REVERT: G 67 ASN cc_start: 0.8756 (m-40) cc_final: 0.8487 (t0) REVERT: G 74 CYS cc_start: 0.7829 (m) cc_final: 0.7453 (m) REVERT: G 95 MET cc_start: 0.7368 (ptp) cc_final: 0.7141 (ptp) REVERT: G 420 ILE cc_start: 0.9244 (mp) cc_final: 0.8953 (mt) REVERT: G 434 MET cc_start: 0.8331 (ttm) cc_final: 0.8013 (ttm) REVERT: I 530 MET cc_start: 0.7266 (mmm) cc_final: 0.6788 (mmm) REVERT: I 602 ILE cc_start: 0.9513 (mm) cc_final: 0.9114 (tp) REVERT: I 629 MET cc_start: 0.8509 (mmm) cc_final: 0.7758 (mmm) REVERT: J 42 GLN cc_start: 0.7444 (mp10) cc_final: 0.6935 (mp10) REVERT: J 75 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8661 (tp) REVERT: J 82 ASP cc_start: 0.6101 (p0) cc_final: 0.5732 (p0) REVERT: K 6 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5510 (mp0) REVERT: K 15 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8351 (tp30) REVERT: K 28 ASP cc_start: 0.7375 (t0) cc_final: 0.6979 (t0) REVERT: K 30 SER cc_start: 0.9143 (m) cc_final: 0.8791 (m) REVERT: K 38 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8285 (ttm170) outliers start: 71 outliers final: 51 residues processed: 400 average time/residue: 0.1413 time to fit residues: 89.9267 Evaluate side-chains 377 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 321 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 38 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 51 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.071695 restraints weight = 52687.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074381 restraints weight = 30637.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076205 restraints weight = 21591.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077467 restraints weight = 17170.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078267 restraints weight = 14617.929| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21003 Z= 0.177 Angle : 0.724 16.173 28770 Z= 0.351 Chirality : 0.046 0.265 3516 Planarity : 0.004 0.040 3465 Dihedral : 5.556 33.541 5019 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.71 % Allowed : 17.49 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.41 (0.17), residues: 2364 helix: 0.70 (0.28), residues: 366 sheet: 0.38 (0.19), residues: 705 loop : -0.92 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 94 TYR 0.022 0.002 TYR K 58 PHE 0.025 0.002 PHE H 47 TRP 0.067 0.002 TRP H 36 HIS 0.015 0.001 HIS K 33 Details of bonding type rmsd covalent geometry : bond 0.00409 (20853) covalent geometry : angle 0.69560 (28353) SS BOND : bond 0.00229 ( 33) SS BOND : angle 0.68932 ( 66) hydrogen bonds : bond 0.04567 ( 720) hydrogen bonds : angle 5.34197 ( 1980) link_ALPHA1-3 : bond 0.00899 ( 3) link_ALPHA1-3 : angle 1.90974 ( 9) link_BETA1-4 : bond 0.00577 ( 45) link_BETA1-4 : angle 1.46857 ( 135) link_NAG-ASN : bond 0.00489 ( 69) link_NAG-ASN : angle 2.20720 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 330 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8589 (ttm) REVERT: A 373 THR cc_start: 0.8626 (p) cc_final: 0.8348 (p) REVERT: A 420 ILE cc_start: 0.9200 (mp) cc_final: 0.8881 (mt) REVERT: A 479 TRP cc_start: 0.8407 (m-10) cc_final: 0.8040 (m-90) REVERT: B 530 MET cc_start: 0.7406 (mmm) cc_final: 0.7113 (mmm) REVERT: B 621 GLU cc_start: 0.8658 (tt0) cc_final: 0.8362 (tt0) REVERT: L 4 MET cc_start: 0.7081 (tpp) cc_final: 0.6196 (tpp) REVERT: L 42 GLN cc_start: 0.7289 (mp10) cc_final: 0.6814 (mp-120) REVERT: L 75 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8437 (tp) REVERT: L 82 ASP cc_start: 0.6134 (p0) cc_final: 0.5789 (p0) REVERT: L 95 ASP cc_start: 0.7465 (m-30) cc_final: 0.7137 (m-30) REVERT: H 13 GLN cc_start: 0.8488 (pp30) cc_final: 0.8122 (pp30) REVERT: H 15 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8213 (tp30) REVERT: H 31 ASP cc_start: 0.8691 (p0) cc_final: 0.8417 (p0) REVERT: H 46 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6904 (mp0) REVERT: C 74 CYS cc_start: 0.7799 (m) cc_final: 0.7478 (m) REVERT: C 420 ILE cc_start: 0.9105 (mp) cc_final: 0.8792 (mt) REVERT: C 479 TRP cc_start: 0.8374 (m-10) cc_final: 0.8153 (m-90) REVERT: D 595 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9095 (tp) REVERT: D 602 ILE cc_start: 0.9503 (mm) cc_final: 0.9208 (tp) REVERT: D 621 GLU cc_start: 0.8783 (tt0) cc_final: 0.8402 (tt0) REVERT: E 4 MET cc_start: 0.7278 (mmm) cc_final: 0.6218 (tpp) REVERT: E 42 GLN cc_start: 0.7543 (mp10) cc_final: 0.7163 (mp10) REVERT: E 75 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8451 (tp) REVERT: E 82 ASP cc_start: 0.6025 (p0) cc_final: 0.5674 (p0) REVERT: F 28 ASP cc_start: 0.7114 (t0) cc_final: 0.6712 (t0) REVERT: F 30 SER cc_start: 0.9118 (m) cc_final: 0.8792 (m) REVERT: F 31 ASP cc_start: 0.8814 (p0) cc_final: 0.8523 (p0) REVERT: F 38 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7853 (ttm170) REVERT: G 67 ASN cc_start: 0.8769 (m-40) cc_final: 0.8509 (t0) REVERT: G 74 CYS cc_start: 0.7854 (m) cc_final: 0.7452 (m) REVERT: G 95 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7254 (ptp) REVERT: G 420 ILE cc_start: 0.9270 (mp) cc_final: 0.8994 (mt) REVERT: G 434 MET cc_start: 0.8483 (ttm) cc_final: 0.8010 (ttm) REVERT: I 530 MET cc_start: 0.7339 (mmm) cc_final: 0.6894 (mmm) REVERT: I 595 ILE cc_start: 0.9462 (tp) cc_final: 0.9011 (tp) REVERT: I 602 ILE cc_start: 0.9505 (mm) cc_final: 0.9126 (tp) REVERT: J 42 GLN cc_start: 0.7456 (mp10) cc_final: 0.6955 (mp10) REVERT: J 63 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8136 (mmtt) REVERT: J 75 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8479 (tp) REVERT: J 82 ASP cc_start: 0.6155 (p0) cc_final: 0.5844 (p0) REVERT: K 6 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5786 (mp0) REVERT: K 15 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8360 (tp30) REVERT: K 28 ASP cc_start: 0.7452 (t0) cc_final: 0.7065 (t0) REVERT: K 30 SER cc_start: 0.9124 (m) cc_final: 0.8720 (m) REVERT: K 31 ASP cc_start: 0.8606 (p0) cc_final: 0.8315 (p0) REVERT: K 38 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8153 (ttm-80) outliers start: 77 outliers final: 57 residues processed: 371 average time/residue: 0.1447 time to fit residues: 85.4712 Evaluate side-chains 373 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 308 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 22 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 46 optimal weight: 0.0030 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.074143 restraints weight = 53365.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076920 restraints weight = 30993.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078794 restraints weight = 21758.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080059 restraints weight = 17210.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080957 restraints weight = 14691.597| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21003 Z= 0.128 Angle : 0.707 16.451 28770 Z= 0.342 Chirality : 0.046 0.246 3516 Planarity : 0.004 0.041 3465 Dihedral : 5.229 33.949 5019 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.89 % Allowed : 18.45 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.38 (0.17), residues: 2364 helix: 0.59 (0.27), residues: 372 sheet: 0.42 (0.20), residues: 705 loop : -0.89 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 273 TYR 0.022 0.001 TYR K 58 PHE 0.016 0.002 PHE E 98 TRP 0.057 0.002 TRP F 36 HIS 0.012 0.001 HIS K 33 Details of bonding type rmsd covalent geometry : bond 0.00285 (20853) covalent geometry : angle 0.68030 (28353) SS BOND : bond 0.00335 ( 33) SS BOND : angle 0.94260 ( 66) hydrogen bonds : bond 0.04283 ( 720) hydrogen bonds : angle 5.25915 ( 1980) link_ALPHA1-3 : bond 0.00842 ( 3) link_ALPHA1-3 : angle 1.72201 ( 9) link_BETA1-4 : bond 0.00588 ( 45) link_BETA1-4 : angle 1.41031 ( 135) link_NAG-ASN : bond 0.00378 ( 69) link_NAG-ASN : angle 2.10070 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 350 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8606 (ttm) REVERT: A 373 THR cc_start: 0.8577 (p) cc_final: 0.8299 (p) REVERT: A 420 ILE cc_start: 0.9156 (mp) cc_final: 0.8862 (mt) REVERT: A 479 TRP cc_start: 0.8326 (m-10) cc_final: 0.7975 (m-90) REVERT: B 530 MET cc_start: 0.7232 (mmm) cc_final: 0.6894 (mmm) REVERT: B 621 GLU cc_start: 0.8634 (tt0) cc_final: 0.8297 (tt0) REVERT: L 42 GLN cc_start: 0.7526 (mp10) cc_final: 0.7122 (mp10) REVERT: L 75 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8556 (tp) REVERT: L 82 ASP cc_start: 0.6076 (p0) cc_final: 0.5775 (p0) REVERT: H 13 GLN cc_start: 0.8487 (pp30) cc_final: 0.8150 (pp30) REVERT: H 15 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8198 (tp30) REVERT: H 28 ASP cc_start: 0.7488 (t0) cc_final: 0.7202 (t0) REVERT: H 30 SER cc_start: 0.9014 (m) cc_final: 0.8805 (m) REVERT: H 31 ASP cc_start: 0.8754 (p0) cc_final: 0.8436 (p0) REVERT: C 74 CYS cc_start: 0.7808 (m) cc_final: 0.7395 (m) REVERT: C 420 ILE cc_start: 0.9137 (mp) cc_final: 0.8842 (mt) REVERT: D 542 ARG cc_start: 0.6805 (ttt180) cc_final: 0.5656 (mmt180) REVERT: D 595 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9017 (tp) REVERT: D 602 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9174 (tp) REVERT: D 621 GLU cc_start: 0.8729 (tt0) cc_final: 0.8460 (tt0) REVERT: D 622 ILE cc_start: 0.8932 (mt) cc_final: 0.8576 (mt) REVERT: E 4 MET cc_start: 0.7128 (mmm) cc_final: 0.6200 (tpp) REVERT: E 42 GLN cc_start: 0.7325 (mp10) cc_final: 0.6962 (mp10) REVERT: E 75 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8475 (tp) REVERT: E 82 ASP cc_start: 0.5875 (p0) cc_final: 0.5611 (p0) REVERT: F 30 SER cc_start: 0.9129 (m) cc_final: 0.8861 (m) REVERT: F 31 ASP cc_start: 0.8828 (p0) cc_final: 0.8368 (p0) REVERT: F 32 TYR cc_start: 0.8668 (m-80) cc_final: 0.8333 (m-10) REVERT: F 35 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6465 (mt0) REVERT: F 38 ARG cc_start: 0.8256 (ttp-170) cc_final: 0.7885 (ttm170) REVERT: G 74 CYS cc_start: 0.7785 (m) cc_final: 0.7399 (m) REVERT: G 420 ILE cc_start: 0.9227 (mp) cc_final: 0.8955 (mt) REVERT: G 434 MET cc_start: 0.8391 (ttm) cc_final: 0.7954 (ttm) REVERT: I 530 MET cc_start: 0.7250 (mmm) cc_final: 0.6755 (mmm) REVERT: I 542 ARG cc_start: 0.6625 (ttt180) cc_final: 0.5407 (mmt180) REVERT: I 595 ILE cc_start: 0.9434 (tp) cc_final: 0.9028 (tp) REVERT: I 602 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9201 (tp) REVERT: J 42 GLN cc_start: 0.7524 (mp10) cc_final: 0.7129 (mp10) REVERT: J 63 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8257 (mmtt) REVERT: J 82 ASP cc_start: 0.6074 (p0) cc_final: 0.5848 (p0) REVERT: K 6 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: K 15 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8345 (tp30) REVERT: K 28 ASP cc_start: 0.7502 (t0) cc_final: 0.7147 (t0) REVERT: K 30 SER cc_start: 0.9127 (m) cc_final: 0.8701 (m) REVERT: K 31 ASP cc_start: 0.8639 (p0) cc_final: 0.8280 (p0) REVERT: K 57 ILE cc_start: 0.9556 (pt) cc_final: 0.9299 (mp) outliers start: 60 outliers final: 39 residues processed: 378 average time/residue: 0.1444 time to fit residues: 86.0583 Evaluate side-chains 361 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 602 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 104 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.0070 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073872 restraints weight = 52729.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076565 restraints weight = 30643.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078401 restraints weight = 21624.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079660 restraints weight = 17108.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080445 restraints weight = 14583.537| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.003 0.043 21003 Z= 0.139 Angle : 0.716 16.442 28770 Z= 0.348 Chirality : 0.046 0.291 3516 Planarity : 0.004 0.048 3465 Dihedral : 5.146 35.161 5019 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.50 % Allowed : 19.41 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.37 (0.17), residues: 2364 helix: 0.51 (0.27), residues: 372 sheet: 0.47 (0.19), residues: 720 loop : -0.89 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 456 TYR 0.012 0.001 TYR A 39 PHE 0.040 0.002 PHE K 47 TRP 0.075 0.002 TRP F 36 HIS 0.009 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00317 (20853) covalent geometry : angle 0.68926 (28353) SS BOND : bond 0.00339 ( 33) SS BOND : angle 1.23500 ( 66) hydrogen bonds : bond 0.04233 ( 720) hydrogen bonds : angle 5.25314 ( 1980) link_ALPHA1-3 : bond 0.00791 ( 3) link_ALPHA1-3 : angle 1.58984 ( 9) link_BETA1-4 : bond 0.00552 ( 45) link_BETA1-4 : angle 1.38634 ( 135) link_NAG-ASN : bond 0.00368 ( 69) link_NAG-ASN : angle 2.07281 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 330 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8647 (ttm) REVERT: A 373 THR cc_start: 0.8588 (p) cc_final: 0.8301 (p) REVERT: A 420 ILE cc_start: 0.9171 (mp) cc_final: 0.8882 (mt) REVERT: A 475 MET cc_start: 0.7958 (mmp) cc_final: 0.7720 (mmm) REVERT: A 479 TRP cc_start: 0.8343 (m-10) cc_final: 0.8050 (m-90) REVERT: B 530 MET cc_start: 0.7229 (mmm) cc_final: 0.6846 (mmm) REVERT: B 621 GLU cc_start: 0.8641 (tt0) cc_final: 0.8347 (tt0) REVERT: L 75 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8539 (tp) REVERT: L 82 ASP cc_start: 0.6055 (p0) cc_final: 0.5719 (p0) REVERT: H 13 GLN cc_start: 0.8450 (pp30) cc_final: 0.8139 (pp30) REVERT: H 15 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8189 (tp30) REVERT: H 31 ASP cc_start: 0.8777 (p0) cc_final: 0.8423 (p0) REVERT: C 74 CYS cc_start: 0.7836 (m) cc_final: 0.7371 (m) REVERT: C 116 LEU cc_start: 0.8829 (tp) cc_final: 0.8586 (tp) REVERT: C 420 ILE cc_start: 0.9059 (mp) cc_final: 0.8779 (mt) REVERT: C 479 TRP cc_start: 0.8343 (m-10) cc_final: 0.8037 (m-90) REVERT: D 542 ARG cc_start: 0.6812 (ttt180) cc_final: 0.5705 (mmt180) REVERT: D 595 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9035 (tp) REVERT: D 629 MET cc_start: 0.8612 (mmm) cc_final: 0.7705 (mmm) REVERT: E 4 MET cc_start: 0.7321 (mmm) cc_final: 0.6510 (tpp) REVERT: E 42 GLN cc_start: 0.7343 (mp10) cc_final: 0.6990 (mp10) REVERT: E 82 ASP cc_start: 0.5868 (p0) cc_final: 0.5623 (p0) REVERT: F 31 ASP cc_start: 0.8820 (p0) cc_final: 0.8360 (p0) REVERT: F 32 TYR cc_start: 0.8762 (m-80) cc_final: 0.8448 (m-10) REVERT: F 68 THR cc_start: 0.8171 (m) cc_final: 0.7788 (p) REVERT: G 74 CYS cc_start: 0.7769 (m) cc_final: 0.7352 (m) REVERT: G 420 ILE cc_start: 0.9209 (mp) cc_final: 0.8934 (mt) REVERT: G 434 MET cc_start: 0.8353 (ttm) cc_final: 0.7863 (ttm) REVERT: I 530 MET cc_start: 0.7175 (mmm) cc_final: 0.6796 (mmm) REVERT: I 542 ARG cc_start: 0.6619 (ttt180) cc_final: 0.5423 (mmt180) REVERT: I 595 ILE cc_start: 0.9442 (tp) cc_final: 0.9094 (tp) REVERT: I 602 ILE cc_start: 0.9501 (mm) cc_final: 0.9239 (tp) REVERT: I 629 MET cc_start: 0.8562 (tpp) cc_final: 0.8007 (tpp) REVERT: J 42 GLN cc_start: 0.7454 (mp10) cc_final: 0.7075 (mp10) REVERT: J 82 ASP cc_start: 0.6045 (p0) cc_final: 0.5808 (p0) REVERT: J 103 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7752 (pp20) REVERT: K 6 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5596 (mp0) REVERT: K 15 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8332 (tp30) REVERT: K 28 ASP cc_start: 0.7557 (t0) cc_final: 0.7204 (t0) REVERT: K 30 SER cc_start: 0.9132 (m) cc_final: 0.8697 (m) REVERT: K 31 ASP cc_start: 0.8686 (p0) cc_final: 0.8313 (p0) REVERT: K 46 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7116 (mp0) REVERT: K 62 TRP cc_start: 0.8392 (t-100) cc_final: 0.8129 (t-100) outliers start: 52 outliers final: 41 residues processed: 362 average time/residue: 0.1399 time to fit residues: 80.5289 Evaluate side-chains 351 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 306 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 425 ASN Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 85 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 0.0980 chunk 161 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.072985 restraints weight = 52932.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075644 restraints weight = 30700.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077452 restraints weight = 21613.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078673 restraints weight = 17118.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079520 restraints weight = 14614.664| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21003 Z= 0.165 Angle : 0.740 16.369 28770 Z= 0.361 Chirality : 0.046 0.323 3516 Planarity : 0.004 0.078 3465 Dihedral : 5.189 35.237 5019 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.46 % Allowed : 19.75 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.43 (0.17), residues: 2364 helix: 0.52 (0.27), residues: 372 sheet: 0.31 (0.19), residues: 738 loop : -0.87 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 38 TYR 0.029 0.001 TYR H 32 PHE 0.035 0.002 PHE K 47 TRP 0.067 0.003 TRP K 36 HIS 0.011 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00384 (20853) covalent geometry : angle 0.71476 (28353) SS BOND : bond 0.00318 ( 33) SS BOND : angle 1.16958 ( 66) hydrogen bonds : bond 0.04362 ( 720) hydrogen bonds : angle 5.29452 ( 1980) link_ALPHA1-3 : bond 0.00757 ( 3) link_ALPHA1-3 : angle 1.59637 ( 9) link_BETA1-4 : bond 0.00527 ( 45) link_BETA1-4 : angle 1.40248 ( 135) link_NAG-ASN : bond 0.00375 ( 69) link_NAG-ASN : angle 2.08646 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8657 (ttm) REVERT: A 373 THR cc_start: 0.8635 (p) cc_final: 0.8348 (p) REVERT: A 420 ILE cc_start: 0.9160 (mp) cc_final: 0.8865 (mt) REVERT: A 475 MET cc_start: 0.7915 (mmp) cc_final: 0.7632 (mmm) REVERT: A 479 TRP cc_start: 0.8339 (m-10) cc_final: 0.8014 (m-90) REVERT: B 530 MET cc_start: 0.7304 (mmm) cc_final: 0.7011 (mmm) REVERT: B 621 GLU cc_start: 0.8630 (tt0) cc_final: 0.8317 (tt0) REVERT: L 75 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8527 (tp) REVERT: L 82 ASP cc_start: 0.6142 (p0) cc_final: 0.5808 (p0) REVERT: H 15 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8117 (tp30) REVERT: H 31 ASP cc_start: 0.8811 (p0) cc_final: 0.8560 (p0) REVERT: C 74 CYS cc_start: 0.7867 (m) cc_final: 0.7403 (m) REVERT: C 95 MET cc_start: 0.7682 (ptp) cc_final: 0.7277 (ptp) REVERT: C 116 LEU cc_start: 0.8862 (tp) cc_final: 0.8628 (tp) REVERT: C 420 ILE cc_start: 0.9086 (mp) cc_final: 0.8796 (mt) REVERT: D 542 ARG cc_start: 0.6842 (ttt180) cc_final: 0.5731 (mmt180) REVERT: D 595 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9034 (tp) REVERT: D 602 ILE cc_start: 0.9479 (mm) cc_final: 0.9241 (tp) REVERT: D 629 MET cc_start: 0.8593 (mmm) cc_final: 0.7710 (mmm) REVERT: E 42 GLN cc_start: 0.7325 (mp10) cc_final: 0.6979 (mp10) REVERT: E 82 ASP cc_start: 0.5698 (p0) cc_final: 0.5450 (p0) REVERT: F 31 ASP cc_start: 0.8799 (p0) cc_final: 0.8270 (p0) REVERT: F 32 TYR cc_start: 0.8829 (m-80) cc_final: 0.8522 (m-10) REVERT: F 68 THR cc_start: 0.8064 (m) cc_final: 0.7688 (p) REVERT: G 74 CYS cc_start: 0.7841 (m) cc_final: 0.7397 (m) REVERT: G 420 ILE cc_start: 0.9234 (mp) cc_final: 0.8955 (mt) REVERT: G 434 MET cc_start: 0.8429 (ttm) cc_final: 0.7945 (ttm) REVERT: I 530 MET cc_start: 0.7154 (mmm) cc_final: 0.6770 (mmm) REVERT: I 542 ARG cc_start: 0.6630 (ttt180) cc_final: 0.5419 (mmt180) REVERT: I 602 ILE cc_start: 0.9516 (mm) cc_final: 0.9274 (tp) REVERT: I 629 MET cc_start: 0.8688 (tpp) cc_final: 0.7929 (mmm) REVERT: J 42 GLN cc_start: 0.7443 (mp10) cc_final: 0.7085 (mp10) REVERT: J 63 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8169 (mmtt) REVERT: J 82 ASP cc_start: 0.6250 (p0) cc_final: 0.5992 (p0) REVERT: K 6 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: K 15 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8357 (tp30) REVERT: K 28 ASP cc_start: 0.7582 (t0) cc_final: 0.7225 (t0) REVERT: K 30 SER cc_start: 0.9021 (m) cc_final: 0.8563 (m) REVERT: K 31 ASP cc_start: 0.8736 (p0) cc_final: 0.8407 (p0) REVERT: K 62 TRP cc_start: 0.8505 (t-100) cc_final: 0.8261 (t-100) outliers start: 51 outliers final: 44 residues processed: 346 average time/residue: 0.1334 time to fit residues: 73.4228 Evaluate side-chains 351 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100EGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.072608 restraints weight = 53049.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075286 restraints weight = 30939.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077127 restraints weight = 21866.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078360 restraints weight = 17306.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079211 restraints weight = 14800.921| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21003 Z= 0.153 Angle : 0.735 16.443 28770 Z= 0.356 Chirality : 0.046 0.269 3516 Planarity : 0.004 0.045 3465 Dihedral : 5.165 35.218 5019 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.60 % Allowed : 19.75 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.43 (0.17), residues: 2364 helix: 0.57 (0.27), residues: 372 sheet: 0.27 (0.19), residues: 741 loop : -0.87 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 38 TYR 0.019 0.001 TYR H 90 PHE 0.031 0.002 PHE K 47 TRP 0.073 0.002 TRP K 36 HIS 0.009 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00354 (20853) covalent geometry : angle 0.70941 (28353) SS BOND : bond 0.00301 ( 33) SS BOND : angle 1.21629 ( 66) hydrogen bonds : bond 0.04330 ( 720) hydrogen bonds : angle 5.28603 ( 1980) link_ALPHA1-3 : bond 0.00726 ( 3) link_ALPHA1-3 : angle 1.55948 ( 9) link_BETA1-4 : bond 0.00521 ( 45) link_BETA1-4 : angle 1.38397 ( 135) link_NAG-ASN : bond 0.00353 ( 69) link_NAG-ASN : angle 2.06327 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.23 seconds wall clock time: 61 minutes 10.87 seconds (3670.87 seconds total)