Starting phenix.real_space_refine on Fri Jul 3 20:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8c_23229/07_2026/7l8c_23229.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 99 5.16 5 C 9921 2.51 5 N 2654 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15963 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "E" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "D" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 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 chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 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 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 chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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 chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 chiralities: 2 Time building chain proxies: 4.32, per 1000 atoms: 0.27 Number of scatterers: 15963 At special positions: 0 Unit cell: (128.75, 127.72, 152.44, 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 99 16.00 O 3289 8.00 N 2654 7.00 C 9921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 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=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.12 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.09 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.09 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.13 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.07 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.01 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA n 3 " - " MAN n 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 133 " " NAG A 605 " - " ASN A 355 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 137 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 339 " " NAG D 603 " - " ASN D 137 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 197 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 332 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 88 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 392 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 133 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 197 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 276 " " NAG a 1 " - " ASN C 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 386 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN C 88 " " NAG f 1 " - " ASN C 160 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 301 " " NAG i 1 " - " ASN E 611 " " NAG j 1 " - " ASN E 618 " " NAG k 1 " - " ASN D 133 " " NAG l 1 " - " ASN D 156 " " NAG m 1 " - " ASN D 197 " " NAG n 1 " - " ASN D 262 " " NAG o 1 " - " ASN D 276 " " NAG p 1 " - " ASN D 295 " " NAG q 1 " - " ASN D 332 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 392 " " NAG t 1 " - " ASN D 448 " " NAG u 1 " - " ASN D 88 " " NAG v 1 " - " ASN D 234 " " NAG w 1 " - " ASN D 301 " " NAG x 1 " - " ASN F 611 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 467.5 milliseconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3606 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 35 sheets defined 28.5% alpha, 49.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.151A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.530A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.354A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.534A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.782A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.151A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.552A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.231A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.775A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.094A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.304A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.826A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 98 through 102 removed outlier: 4.307A pdb=" N UNK H 102 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.470A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.863A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 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 200 through 203 removed outlier: 6.213A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.449A 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: 4.742A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.406A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.406A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.543A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.253A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.767A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.007A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.683A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.683A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.683A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.660A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.382A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.823A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AC6, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC7, first strand: chain 'D' and resid 169 through 176 Processing sheet with id=AC8, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.104A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.728A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.728A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.728A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.860A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.754A pdb=" N UNK H 73 " --> pdb=" O UNK H 68 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 55 through 57 removed outlier: 5.887A pdb=" N UNK H 45 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N UNK H 37 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N UNK H 91 " --> pdb=" O UNK H 108 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N UNK H 108 " --> pdb=" O UNK H 91 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N UNK H 93 " --> pdb=" O UNK H 106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AD8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.774A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N UNK L 85 " --> pdb=" O UNK L 38 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1731 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: 3.02 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 2531 1.25 - 1.41: 3781 1.41 - 1.56: 9320 1.56 - 1.72: 472 1.72 - 1.87: 130 Bond restraints: 16234 Sorted by residual: bond pdb=" C TRP A 479 " pdb=" O TRP A 479 " ideal model delta sigma weight residual 1.236 1.095 0.141 1.29e-02 6.01e+03 1.19e+02 bond pdb=" C TRP C 479 " pdb=" O TRP C 479 " ideal model delta sigma weight residual 1.236 1.106 0.131 1.29e-02 6.01e+03 1.02e+02 bond pdb=" C TRP D 479 " pdb=" O TRP D 479 " ideal model delta sigma weight residual 1.237 1.124 0.113 1.19e-02 7.06e+03 9.00e+01 bond pdb=" C LYS A 46 " pdb=" O LYS A 46 " ideal model delta sigma weight residual 1.234 1.120 0.114 1.22e-02 6.72e+03 8.67e+01 bond pdb=" C LYS F 574 " pdb=" O LYS F 574 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.15e-02 7.56e+03 6.99e+01 ... (remaining 16229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 19824 2.77 - 5.54: 2039 5.54 - 8.30: 206 8.30 - 11.07: 19 11.07 - 13.84: 2 Bond angle restraints: 22090 Sorted by residual: angle pdb=" N HIS B 570 " pdb=" CA HIS B 570 " pdb=" C HIS B 570 " ideal model delta sigma weight residual 113.55 103.29 10.26 1.26e+00 6.30e-01 6.63e+01 angle pdb=" N THR D 71 " pdb=" CA THR D 71 " pdb=" C THR D 71 " ideal model delta sigma weight residual 114.56 104.67 9.89 1.27e+00 6.20e-01 6.06e+01 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 99.23 11.25 1.48e+00 4.57e-01 5.78e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.16 -7.60 1.01e+00 9.80e-01 5.67e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.10 -7.54 1.01e+00 9.80e-01 5.58e+01 ... (remaining 22085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8578 17.87 - 35.73: 208 35.73 - 53.60: 70 53.60 - 71.46: 25 71.46 - 89.33: 7 Dihedral angle restraints: 8888 sinusoidal: 3346 harmonic: 5542 Sorted by residual: dihedral pdb=" N HIS B 570 " pdb=" C HIS B 570 " pdb=" CA HIS B 570 " pdb=" CB HIS B 570 " ideal model delta harmonic sigma weight residual 122.80 107.74 15.06 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" C HIS B 570 " pdb=" N HIS B 570 " pdb=" CA HIS B 570 " pdb=" CB HIS B 570 " ideal model delta harmonic sigma weight residual -122.60 -109.20 -13.40 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -129.54 43.54 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 8885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1754 0.103 - 0.206: 604 0.206 - 0.309: 293 0.309 - 0.412: 143 0.412 - 0.515: 77 Chirality restraints: 2871 Sorted by residual: chirality pdb=" C1 NAG q 2 " pdb=" O4 NAG q 1 " pdb=" C2 NAG q 2 " pdb=" O5 NAG q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 NAG r 2 " pdb=" O4 NAG r 1 " pdb=" C2 NAG r 2 " pdb=" O5 NAG r 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.62e+02 ... (remaining 2868 not shown) Planarity restraints: 2743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.336 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG C 604 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 2 " 0.260 2.00e-02 2.50e+03 2.19e-01 5.99e+02 pdb=" C7 NAG g 2 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG g 2 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG g 2 " -0.370 2.00e-02 2.50e+03 pdb=" O7 NAG g 2 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 701 " 0.243 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG E 701 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG E 701 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG E 701 " -0.349 2.00e-02 2.50e+03 pdb=" O7 NAG E 701 " 0.182 2.00e-02 2.50e+03 ... (remaining 2740 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 167 2.62 - 3.19: 14014 3.19 - 3.76: 22534 3.76 - 4.33: 33167 4.33 - 4.90: 52037 Nonbonded interactions: 121919 Sorted by model distance: nonbonded pdb=" O3 NAG g 1 " pdb=" O7 NAG g 1 " model vdw 2.049 3.040 nonbonded pdb=" O HIS B 570 " pdb=" N ILE B 573 " model vdw 2.064 3.120 nonbonded pdb=" O THR F 569 " pdb=" OG1 THR F 569 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN C 234 " pdb=" C1 NAG g 1 " model vdw 2.304 2.776 nonbonded pdb=" N LEU A 179 " pdb=" N ASP A 180 " model vdw 2.405 2.560 ... (remaining 121914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 603) selection = (chain 'C' and resid 33 through 603) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 518 through 663 or resid 702)) selection = (chain 'E' and (resid 518 through 663 or resid 701)) selection = (chain 'F' and (resid 518 through 663 or resid 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain 'H' and resid 8 through 114) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'Y' selection = chain 'j' selection = chain 'l' } 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 individual isotropic 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: 4.040 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.100 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 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 : 0.026 0.339 16378 Z= 1.389 Angle : 1.803 25.741 22489 Z= 1.102 Chirality : 0.159 0.515 2871 Planarity : 0.012 0.292 2684 Dihedral : 10.041 89.326 5183 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1655 helix: -0.02 (0.23), residues: 431 sheet: 1.30 (0.24), residues: 405 loop : 0.45 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 166 TYR 0.048 0.007 TYR D 484 PHE 0.034 0.006 PHE D 383 TRP 0.056 0.010 TRP A 35 HIS 0.020 0.003 HIS F 570 Details of bonding type rmsd/Z covalent geometry : bond 0.02564 / 1.35 (16234) covalent geometry : angle 1.74047 / 1.10 (22090) SS BOND : bond 0.03334 / 1.83 ( 33) SS BOND : angle 2.90155 / 2.12 ( 66) hydrogen bonds : bond 0.17689 / 12.07 ( 607) hydrogen bonds : angle 7.35949 / 5.20 ( 1731) link_ALPHA1-3 : bond 0.08037 / 4.04 ( 2) link_ALPHA1-3 : angle 4.31503 / 3.55 ( 6) link_ALPHA1-6 : bond 0.04712 / 2.37 ( 2) link_ALPHA1-6 : angle 3.10052 / 2.36 ( 6) link_BETA1-4 : bond 0.07043 / 4.45 ( 48) link_BETA1-4 : angle 4.86759 / 3.53 ( 144) link_NAG-ASN : bond 0.08563 / 5.48 ( 59) link_NAG-ASN : angle 3.37905 / 2.06 ( 177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8449 (mmtt) cc_final: 0.7979 (tmtt) REVERT: A 464 THR cc_start: 0.7658 (p) cc_final: 0.7389 (t) REVERT: E 616 ASN cc_start: 0.8606 (t0) cc_final: 0.8219 (t0) REVERT: E 624 ASP cc_start: 0.8500 (m-30) cc_final: 0.8276 (m-30) REVERT: E 632 ASP cc_start: 0.8723 (t70) cc_final: 0.8516 (t0) REVERT: D 102 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8422 (mm-30) REVERT: D 207 LYS cc_start: 0.8717 (pttt) cc_final: 0.8316 (mmtt) REVERT: D 232 LYS cc_start: 0.8603 (mttt) cc_final: 0.8400 (mttp) REVERT: D 462 ASN cc_start: 0.7484 (t0) cc_final: 0.7150 (p0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1495 time to fit residues: 67.6295 Evaluate side-chains 165 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 590 GLN B 630 GLN B 653 GLN D 114 GLN D 374 HIS F 575 GLN F 607 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096277 restraints weight = 25516.461| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.69 r_work: 0.2948 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16378 Z= 0.174 Angle : 0.752 13.933 22489 Z= 0.366 Chirality : 0.046 0.294 2871 Planarity : 0.004 0.031 2684 Dihedral : 4.842 31.414 2005 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.20 % Allowed : 5.78 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1655 helix: 1.73 (0.26), residues: 413 sheet: 0.82 (0.23), residues: 465 loop : 0.42 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 151 TYR 0.010 0.001 TYR C 191 PHE 0.014 0.002 PHE A 353 TRP 0.024 0.002 TRP B 571 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16234) covalent geometry : angle 0.69094 / 0.35 (22090) SS BOND : bond 0.00371 / 0.22 ( 33) SS BOND : angle 1.50006 / 0.95 ( 66) hydrogen bonds : bond 0.06338 / 4.25 ( 607) hydrogen bonds : angle 5.65411 / 3.98 ( 1731) link_ALPHA1-3 : bond 0.00567 / 0.29 ( 2) link_ALPHA1-3 : angle 1.78063 / 1.08 ( 6) link_ALPHA1-6 : bond 0.00598 / 0.31 ( 2) link_ALPHA1-6 : angle 1.33022 / 0.81 ( 6) link_BETA1-4 : bond 0.00510 / 0.31 ( 48) link_BETA1-4 : angle 2.43401 / 1.84 ( 144) link_NAG-ASN : bond 0.00480 / 0.30 ( 59) link_NAG-ASN : angle 2.54045 / 1.76 ( 177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7757 (tmtt) REVERT: A 210 PHE cc_start: 0.8873 (m-80) cc_final: 0.8613 (m-80) REVERT: A 484 TYR cc_start: 0.9251 (p90) cc_final: 0.8766 (p90) REVERT: B 575 GLN cc_start: 0.8236 (tp40) cc_final: 0.8010 (tt0) REVERT: B 620 SER cc_start: 0.9094 (m) cc_final: 0.8808 (t) REVERT: C 82 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8007 (mp10) REVERT: C 475 MET cc_start: 0.8898 (mmt) cc_final: 0.8523 (mmt) REVERT: C 503 ARG cc_start: 0.8059 (mmp-170) cc_final: 0.7765 (tpp-160) REVERT: E 616 ASN cc_start: 0.8961 (t0) cc_final: 0.8598 (t0) REVERT: E 624 ASP cc_start: 0.8699 (m-30) cc_final: 0.8468 (m-30) REVERT: D 215 ILE cc_start: 0.8891 (mt) cc_final: 0.8667 (pt) REVERT: D 373 THR cc_start: 0.9266 (m) cc_final: 0.8511 (p) REVERT: D 462 ASN cc_start: 0.7103 (t0) cc_final: 0.6788 (p0) REVERT: F 617 ARG cc_start: 0.8729 (mtt-85) cc_final: 0.8454 (mtt90) outliers start: 18 outliers final: 9 residues processed: 251 average time/residue: 0.1207 time to fit residues: 45.9216 Evaluate side-chains 184 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 601 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 540 GLN B 658 GLN C 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.092166 restraints weight = 26238.059| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.69 r_work: 0.2878 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16378 Z= 0.205 Angle : 0.686 10.673 22489 Z= 0.333 Chirality : 0.045 0.253 2871 Planarity : 0.004 0.033 2684 Dihedral : 4.714 33.955 2005 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.93 % Allowed : 7.91 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.21), residues: 1655 helix: 1.81 (0.27), residues: 413 sheet: 0.89 (0.24), residues: 429 loop : 0.12 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 151 TYR 0.011 0.001 TYR C 191 PHE 0.018 0.002 PHE E 522 TRP 0.018 0.001 TRP B 571 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (16234) covalent geometry : angle 0.64733 / 0.32 (22090) SS BOND : bond 0.00668 / 0.40 ( 33) SS BOND : angle 1.51259 / 0.96 ( 66) hydrogen bonds : bond 0.05381 / 3.60 ( 607) hydrogen bonds : angle 5.15970 / 3.63 ( 1731) link_ALPHA1-3 : bond 0.00595 / 0.30 ( 2) link_ALPHA1-3 : angle 1.48259 / 1.09 ( 6) link_ALPHA1-6 : bond 0.00517 / 0.27 ( 2) link_ALPHA1-6 : angle 1.32931 / 0.94 ( 6) link_BETA1-4 : bond 0.00560 / 0.36 ( 48) link_BETA1-4 : angle 1.80305 / 1.40 ( 144) link_NAG-ASN : bond 0.00293 / 0.18 ( 59) link_NAG-ASN : angle 1.96433 / 1.38 ( 177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8387 (ptt90) cc_final: 0.8180 (ptm-80) REVERT: A 207 LYS cc_start: 0.8565 (mmtt) cc_final: 0.7759 (tmtt) REVERT: A 210 PHE cc_start: 0.9005 (m-80) cc_final: 0.8765 (m-80) REVERT: A 484 TYR cc_start: 0.9354 (p90) cc_final: 0.8999 (p90) REVERT: B 575 GLN cc_start: 0.8276 (tp40) cc_final: 0.7980 (tp40) REVERT: C 82 GLN cc_start: 0.8528 (mm-40) cc_final: 0.7424 (mp10) REVERT: C 153 GLU cc_start: 0.8757 (tp30) cc_final: 0.8395 (mm-30) REVERT: E 616 ASN cc_start: 0.8946 (t0) cc_final: 0.8483 (t0) REVERT: E 624 ASP cc_start: 0.8674 (m-30) cc_final: 0.8439 (m-30) REVERT: E 648 GLU cc_start: 0.9052 (tt0) cc_final: 0.8824 (tt0) REVERT: D 215 ILE cc_start: 0.8968 (mt) cc_final: 0.8493 (pt) REVERT: D 373 THR cc_start: 0.9275 (m) cc_final: 0.8555 (p) REVERT: D 462 ASN cc_start: 0.7144 (t0) cc_final: 0.6806 (p0) REVERT: F 634 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8130 (tt0) outliers start: 29 outliers final: 18 residues processed: 210 average time/residue: 0.1155 time to fit residues: 36.7592 Evaluate side-chains 184 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 569 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN E 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095420 restraints weight = 25880.595| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.70 r_work: 0.2937 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16378 Z= 0.113 Angle : 0.574 9.396 22489 Z= 0.280 Chirality : 0.042 0.255 2871 Planarity : 0.003 0.031 2684 Dihedral : 4.417 33.086 2005 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.66 % Allowed : 9.30 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1655 helix: 2.41 (0.28), residues: 393 sheet: 0.74 (0.23), residues: 465 loop : 0.16 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 166 TYR 0.010 0.001 TYR C 191 PHE 0.009 0.001 PHE D 53 TRP 0.013 0.001 TRP B 571 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16234) covalent geometry : angle 0.53840 / 0.27 (22090) SS BOND : bond 0.00404 / 0.24 ( 33) SS BOND : angle 1.23283 / 0.78 ( 66) hydrogen bonds : bond 0.04342 / 2.87 ( 607) hydrogen bonds : angle 4.79631 / 3.36 ( 1731) link_ALPHA1-3 : bond 0.00481 / 0.24 ( 2) link_ALPHA1-3 : angle 1.43042 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00462 / 0.24 ( 2) link_ALPHA1-6 : angle 1.39179 / 1.00 ( 6) link_BETA1-4 : bond 0.00462 / 0.29 ( 48) link_BETA1-4 : angle 1.49703 / 1.20 ( 144) link_NAG-ASN : bond 0.00216 / 0.13 ( 59) link_NAG-ASN : angle 1.79633 / 1.26 ( 177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8440 (mmtt) cc_final: 0.7627 (tmtt) REVERT: A 210 PHE cc_start: 0.8987 (m-80) cc_final: 0.8779 (m-80) REVERT: A 381 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8034 (mt-10) REVERT: A 484 TYR cc_start: 0.9348 (p90) cc_final: 0.8993 (p90) REVERT: B 575 GLN cc_start: 0.8013 (tp40) cc_final: 0.7798 (tt0) REVERT: E 540 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8212 (mm-40) REVERT: E 616 ASN cc_start: 0.8880 (t0) cc_final: 0.8463 (t0) REVERT: E 624 ASP cc_start: 0.8634 (m-30) cc_final: 0.8432 (m-30) REVERT: E 648 GLU cc_start: 0.9026 (tt0) cc_final: 0.8819 (tt0) REVERT: D 215 ILE cc_start: 0.8958 (mt) cc_final: 0.8510 (pt) REVERT: D 347 LYS cc_start: 0.8857 (tttt) cc_final: 0.8588 (ttpp) REVERT: D 373 THR cc_start: 0.9238 (m) cc_final: 0.8543 (p) REVERT: D 462 ASN cc_start: 0.6928 (t0) cc_final: 0.6723 (p0) REVERT: F 617 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7854 (mtt90) REVERT: F 634 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7968 (tt0) REVERT: F 655 LYS cc_start: 0.8391 (tptm) cc_final: 0.8161 (tptt) outliers start: 25 outliers final: 19 residues processed: 211 average time/residue: 0.1084 time to fit residues: 34.4522 Evaluate side-chains 191 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 155 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 640 GLN B 652 GLN C 280 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.090202 restraints weight = 26379.546| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.68 r_work: 0.2844 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16378 Z= 0.259 Angle : 0.707 9.471 22489 Z= 0.337 Chirality : 0.046 0.246 2871 Planarity : 0.004 0.031 2684 Dihedral : 4.712 33.355 2005 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.06 % Allowed : 9.70 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1655 helix: 1.76 (0.27), residues: 413 sheet: 0.70 (0.24), residues: 429 loop : -0.20 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 542 TYR 0.011 0.002 TYR D 217 PHE 0.015 0.002 PHE C 317 TRP 0.012 0.001 TRP B 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.26 (16234) covalent geometry : angle 0.67593 / 0.33 (22090) SS BOND : bond 0.00533 / 0.31 ( 33) SS BOND : angle 1.23706 / 0.84 ( 66) hydrogen bonds : bond 0.05472 / 3.69 ( 607) hydrogen bonds : angle 5.12715 / 3.60 ( 1731) link_ALPHA1-3 : bond 0.00406 / 0.20 ( 2) link_ALPHA1-3 : angle 1.48141 / 1.06 ( 6) link_ALPHA1-6 : bond 0.00499 / 0.26 ( 2) link_ALPHA1-6 : angle 1.38016 / 0.97 ( 6) link_BETA1-4 : bond 0.00485 / 0.31 ( 48) link_BETA1-4 : angle 1.69852 / 1.31 ( 144) link_NAG-ASN : bond 0.00326 / 0.19 ( 59) link_NAG-ASN : angle 1.87138 / 1.32 ( 177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8554 (ptt90) cc_final: 0.8201 (ptt90) REVERT: A 207 LYS cc_start: 0.8547 (mmtt) cc_final: 0.7664 (tmtt) REVERT: A 484 TYR cc_start: 0.9388 (p90) cc_final: 0.9068 (p90) REVERT: B 648 GLU cc_start: 0.8579 (tp30) cc_final: 0.8091 (tp30) REVERT: C 111 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9059 (mp) REVERT: E 540 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8241 (mm-40) REVERT: E 616 ASN cc_start: 0.8934 (t0) cc_final: 0.8508 (t0) REVERT: E 624 ASP cc_start: 0.8715 (m-30) cc_final: 0.8439 (m-30) REVERT: E 648 GLU cc_start: 0.9010 (tt0) cc_final: 0.8765 (tt0) REVERT: D 215 ILE cc_start: 0.8970 (mt) cc_final: 0.8489 (pt) REVERT: D 302 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8770 (t0) REVERT: D 373 THR cc_start: 0.9327 (m) cc_final: 0.8672 (p) REVERT: F 634 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8188 (tt0) outliers start: 31 outliers final: 24 residues processed: 189 average time/residue: 0.1177 time to fit residues: 33.8930 Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 540 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.090854 restraints weight = 26480.819| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.83 r_work: 0.2865 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16378 Z= 0.175 Angle : 0.615 9.419 22489 Z= 0.296 Chirality : 0.043 0.247 2871 Planarity : 0.003 0.030 2684 Dihedral : 4.580 34.319 2005 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.39 % Allowed : 10.03 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1655 helix: 1.91 (0.27), residues: 413 sheet: 0.73 (0.24), residues: 459 loop : -0.25 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 617 TYR 0.011 0.001 TYR C 191 PHE 0.009 0.002 PHE C 317 TRP 0.012 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (16234) covalent geometry : angle 0.58262 / 0.29 (22090) SS BOND : bond 0.00464 / 0.27 ( 33) SS BOND : angle 1.29834 / 0.76 ( 66) hydrogen bonds : bond 0.04747 / 3.18 ( 607) hydrogen bonds : angle 4.93683 / 3.46 ( 1731) link_ALPHA1-3 : bond 0.00457 / 0.23 ( 2) link_ALPHA1-3 : angle 1.42698 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00459 / 0.24 ( 2) link_ALPHA1-6 : angle 1.39386 / 1.00 ( 6) link_BETA1-4 : bond 0.00437 / 0.28 ( 48) link_BETA1-4 : angle 1.45741 / 1.13 ( 144) link_NAG-ASN : bond 0.00226 / 0.13 ( 59) link_NAG-ASN : angle 1.79197 / 1.28 ( 177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8442 (ptt90) cc_final: 0.8192 (ptm-80) REVERT: A 207 LYS cc_start: 0.8542 (mmtt) cc_final: 0.7683 (tmtt) REVERT: A 484 TYR cc_start: 0.9339 (p90) cc_final: 0.9006 (p90) REVERT: C 111 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8937 (mp) REVERT: E 616 ASN cc_start: 0.8760 (t0) cc_final: 0.8390 (t0) REVERT: E 624 ASP cc_start: 0.8481 (m-30) cc_final: 0.8201 (m-30) REVERT: E 648 GLU cc_start: 0.8762 (tt0) cc_final: 0.8501 (tt0) REVERT: D 215 ILE cc_start: 0.8902 (mt) cc_final: 0.8390 (pt) REVERT: D 373 THR cc_start: 0.9312 (m) cc_final: 0.8674 (p) REVERT: F 634 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8041 (tt0) REVERT: F 647 GLU cc_start: 0.8136 (tt0) cc_final: 0.7889 (tt0) outliers start: 36 outliers final: 31 residues processed: 188 average time/residue: 0.1286 time to fit residues: 36.6279 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092706 restraints weight = 26239.060| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.83 r_work: 0.2897 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16378 Z= 0.121 Angle : 0.557 9.427 22489 Z= 0.270 Chirality : 0.042 0.252 2871 Planarity : 0.003 0.029 2684 Dihedral : 4.285 28.163 2005 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.93 % Allowed : 11.10 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1655 helix: 2.14 (0.27), residues: 413 sheet: 0.79 (0.24), residues: 459 loop : -0.22 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 542 TYR 0.017 0.001 TYR C 191 PHE 0.009 0.001 PHE E 522 TRP 0.012 0.001 TRP A 96 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (16234) covalent geometry : angle 0.52815 / 0.26 (22090) SS BOND : bond 0.00399 / 0.23 ( 33) SS BOND : angle 1.03899 / 0.64 ( 66) hydrogen bonds : bond 0.04132 / 2.75 ( 607) hydrogen bonds : angle 4.73107 / 3.31 ( 1731) link_ALPHA1-3 : bond 0.00444 / 0.22 ( 2) link_ALPHA1-3 : angle 1.41009 / 1.01 ( 6) link_ALPHA1-6 : bond 0.00415 / 0.22 ( 2) link_ALPHA1-6 : angle 1.38296 / 0.99 ( 6) link_BETA1-4 : bond 0.00432 / 0.27 ( 48) link_BETA1-4 : angle 1.34398 / 1.05 ( 144) link_NAG-ASN : bond 0.00205 / 0.12 ( 59) link_NAG-ASN : angle 1.61705 / 1.14 ( 177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8378 (ptt90) cc_final: 0.8117 (ptm-80) REVERT: A 207 LYS cc_start: 0.8544 (mmtt) cc_final: 0.7697 (tmtt) REVERT: A 484 TYR cc_start: 0.9262 (p90) cc_final: 0.8923 (p90) REVERT: B 633 LYS cc_start: 0.9038 (mttm) cc_final: 0.8753 (mmtm) REVERT: C 111 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8922 (mp) REVERT: E 616 ASN cc_start: 0.8733 (t0) cc_final: 0.8315 (t0) REVERT: E 624 ASP cc_start: 0.8449 (m-30) cc_final: 0.8154 (m-30) REVERT: E 648 GLU cc_start: 0.8742 (tt0) cc_final: 0.8501 (tt0) REVERT: D 215 ILE cc_start: 0.8909 (mt) cc_final: 0.8434 (pt) REVERT: D 347 LYS cc_start: 0.8829 (tttt) cc_final: 0.8539 (ttpp) REVERT: D 373 THR cc_start: 0.9249 (m) cc_final: 0.8587 (p) REVERT: F 655 LYS cc_start: 0.8348 (tptp) cc_final: 0.7890 (mtpt) outliers start: 29 outliers final: 26 residues processed: 203 average time/residue: 0.1323 time to fit residues: 40.4365 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.091958 restraints weight = 26530.800| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.85 r_work: 0.2881 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16378 Z= 0.144 Angle : 0.577 9.447 22489 Z= 0.278 Chirality : 0.042 0.251 2871 Planarity : 0.003 0.029 2684 Dihedral : 4.297 27.954 2005 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.06 % Allowed : 10.70 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1655 helix: 2.10 (0.27), residues: 413 sheet: 0.77 (0.24), residues: 465 loop : -0.23 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 542 TYR 0.016 0.001 TYR C 191 PHE 0.010 0.001 PHE C 53 TRP 0.011 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (16234) covalent geometry : angle 0.54842 / 0.27 (22090) SS BOND : bond 0.00414 / 0.24 ( 33) SS BOND : angle 1.17141 / 0.75 ( 66) hydrogen bonds : bond 0.04281 / 2.86 ( 607) hydrogen bonds : angle 4.72166 / 3.30 ( 1731) link_ALPHA1-3 : bond 0.00431 / 0.22 ( 2) link_ALPHA1-3 : angle 1.43076 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00459 / 0.24 ( 2) link_ALPHA1-6 : angle 1.40758 / 1.01 ( 6) link_BETA1-4 : bond 0.00423 / 0.27 ( 48) link_BETA1-4 : angle 1.36318 / 1.05 ( 144) link_NAG-ASN : bond 0.00208 / 0.12 ( 59) link_NAG-ASN : angle 1.61229 / 1.15 ( 177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8586 (mmtt) cc_final: 0.7729 (tmtt) REVERT: A 484 TYR cc_start: 0.9269 (p90) cc_final: 0.8933 (p90) REVERT: C 111 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8916 (mp) REVERT: E 616 ASN cc_start: 0.8756 (t0) cc_final: 0.8364 (t0) REVERT: E 624 ASP cc_start: 0.8440 (m-30) cc_final: 0.8136 (m-30) REVERT: E 648 GLU cc_start: 0.8767 (tt0) cc_final: 0.8526 (tt0) REVERT: D 215 ILE cc_start: 0.8927 (mt) cc_final: 0.8469 (pt) REVERT: D 347 LYS cc_start: 0.8822 (tttt) cc_final: 0.8524 (ttpp) REVERT: D 373 THR cc_start: 0.9258 (m) cc_final: 0.8620 (p) REVERT: F 634 GLU cc_start: 0.8297 (tt0) cc_final: 0.7803 (tt0) REVERT: F 655 LYS cc_start: 0.8322 (tptp) cc_final: 0.7868 (mtpt) outliers start: 31 outliers final: 27 residues processed: 195 average time/residue: 0.1328 time to fit residues: 38.7760 Evaluate side-chains 194 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.089665 restraints weight = 26633.107| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.83 r_work: 0.2846 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16378 Z= 0.213 Angle : 0.653 9.478 22489 Z= 0.312 Chirality : 0.044 0.247 2871 Planarity : 0.004 0.031 2684 Dihedral : 4.561 30.376 2005 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.19 % Allowed : 10.76 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1655 helix: 1.79 (0.27), residues: 416 sheet: 0.86 (0.25), residues: 423 loop : -0.50 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 298 TYR 0.014 0.001 TYR C 191 PHE 0.013 0.002 PHE F 522 TRP 0.011 0.001 TRP C 96 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (16234) covalent geometry : angle 0.62446 / 0.31 (22090) SS BOND : bond 0.00476 / 0.28 ( 33) SS BOND : angle 1.28026 / 0.82 ( 66) hydrogen bonds : bond 0.04974 / 3.35 ( 607) hydrogen bonds : angle 4.95649 / 3.47 ( 1731) link_ALPHA1-3 : bond 0.00405 / 0.20 ( 2) link_ALPHA1-3 : angle 1.44745 / 1.03 ( 6) link_ALPHA1-6 : bond 0.00449 / 0.23 ( 2) link_ALPHA1-6 : angle 1.39791 / 0.98 ( 6) link_BETA1-4 : bond 0.00431 / 0.28 ( 48) link_BETA1-4 : angle 1.45927 / 1.10 ( 144) link_NAG-ASN : bond 0.00299 / 0.18 ( 59) link_NAG-ASN : angle 1.72223 / 1.23 ( 177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8548 (mmtt) cc_final: 0.7686 (tmtt) REVERT: A 484 TYR cc_start: 0.9273 (p90) cc_final: 0.8947 (p90) REVERT: C 111 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8962 (mp) REVERT: E 616 ASN cc_start: 0.8810 (t0) cc_final: 0.8478 (t0) REVERT: E 624 ASP cc_start: 0.8511 (m-30) cc_final: 0.8173 (m-30) REVERT: E 648 GLU cc_start: 0.8760 (tt0) cc_final: 0.8493 (tt0) REVERT: D 215 ILE cc_start: 0.8933 (mt) cc_final: 0.8448 (pt) REVERT: D 373 THR cc_start: 0.9316 (m) cc_final: 0.8678 (p) REVERT: F 546 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8114 (m) REVERT: F 655 LYS cc_start: 0.8374 (tptp) cc_final: 0.7888 (mtpt) outliers start: 33 outliers final: 28 residues processed: 181 average time/residue: 0.1311 time to fit residues: 35.7308 Evaluate side-chains 183 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 171 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 570 HIS B 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092413 restraints weight = 26341.784| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.83 r_work: 0.2892 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16378 Z= 0.116 Angle : 0.566 9.402 22489 Z= 0.275 Chirality : 0.042 0.252 2871 Planarity : 0.003 0.035 2684 Dihedral : 4.294 27.634 2005 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.79 % Allowed : 11.30 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1655 helix: 2.14 (0.27), residues: 413 sheet: 0.79 (0.25), residues: 441 loop : -0.34 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 166 TYR 0.017 0.001 TYR C 191 PHE 0.009 0.001 PHE C 233 TRP 0.010 0.001 TRP B 571 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16234) covalent geometry : angle 0.53947 / 0.27 (22090) SS BOND : bond 0.00407 / 0.23 ( 33) SS BOND : angle 1.06414 / 0.68 ( 66) hydrogen bonds : bond 0.04092 / 2.73 ( 607) hydrogen bonds : angle 4.69526 / 3.27 ( 1731) link_ALPHA1-3 : bond 0.00464 / 0.23 ( 2) link_ALPHA1-3 : angle 1.40040 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00429 / 0.22 ( 2) link_ALPHA1-6 : angle 1.41190 / 1.01 ( 6) link_BETA1-4 : bond 0.00413 / 0.27 ( 48) link_BETA1-4 : angle 1.27519 / 0.98 ( 144) link_NAG-ASN : bond 0.00187 / 0.11 ( 59) link_NAG-ASN : angle 1.58085 / 1.12 ( 177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8532 (mmtt) cc_final: 0.7743 (tmtt) REVERT: A 484 TYR cc_start: 0.9257 (p90) cc_final: 0.8934 (p90) REVERT: B 660 LEU cc_start: 0.9276 (tt) cc_final: 0.8437 (mt) REVERT: E 616 ASN cc_start: 0.8736 (t0) cc_final: 0.8413 (t0) REVERT: E 624 ASP cc_start: 0.8455 (m-30) cc_final: 0.8128 (m-30) REVERT: E 648 GLU cc_start: 0.8750 (tt0) cc_final: 0.8511 (tt0) REVERT: D 56 SER cc_start: 0.8563 (t) cc_final: 0.8299 (p) REVERT: D 161 MET cc_start: 0.8929 (tpt) cc_final: 0.8515 (tpt) REVERT: D 215 ILE cc_start: 0.8898 (mt) cc_final: 0.8422 (pt) REVERT: D 347 LYS cc_start: 0.8807 (tttt) cc_final: 0.8505 (ttpp) REVERT: D 373 THR cc_start: 0.9254 (m) cc_final: 0.8624 (p) REVERT: F 546 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8116 (m) REVERT: F 655 LYS cc_start: 0.8301 (tptp) cc_final: 0.7859 (mtpt) outliers start: 27 outliers final: 24 residues processed: 188 average time/residue: 0.1270 time to fit residues: 36.2719 Evaluate side-chains 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.090061 restraints weight = 26373.449| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.83 r_work: 0.2854 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16378 Z= 0.199 Angle : 0.631 9.474 22489 Z= 0.302 Chirality : 0.044 0.246 2871 Planarity : 0.004 0.067 2684 Dihedral : 4.475 29.487 2005 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.86 % Allowed : 11.23 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1655 helix: 1.90 (0.27), residues: 413 sheet: 0.74 (0.24), residues: 459 loop : -0.39 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 166 TYR 0.015 0.001 TYR A 173 PHE 0.011 0.002 PHE C 317 TRP 0.011 0.001 TRP F 631 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (16234) covalent geometry : angle 0.60430 / 0.30 (22090) SS BOND : bond 0.00453 / 0.27 ( 33) SS BOND : angle 1.16019 / 0.75 ( 66) hydrogen bonds : bond 0.04757 / 3.20 ( 607) hydrogen bonds : angle 4.89515 / 3.43 ( 1731) link_ALPHA1-3 : bond 0.00408 / 0.20 ( 2) link_ALPHA1-3 : angle 1.44248 / 1.03 ( 6) link_ALPHA1-6 : bond 0.00440 / 0.23 ( 2) link_ALPHA1-6 : angle 1.38779 / 0.98 ( 6) link_BETA1-4 : bond 0.00418 / 0.27 ( 48) link_BETA1-4 : angle 1.40634 / 1.05 ( 144) link_NAG-ASN : bond 0.00267 / 0.16 ( 59) link_NAG-ASN : angle 1.66168 / 1.18 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3151.24 seconds wall clock time: 55 minutes 5.78 seconds (3305.78 seconds total)