Starting phenix.real_space_refine on Fri Jul 3 20:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l89_23226/07_2026/7l89_23226.cif" } resolution = 3.8 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= 0.002 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 9758 2.51 5 N 2618 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 15679 Number of models: 1 Model: "" Number of chains: 51 Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 570 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 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: 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: 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: 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: "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: 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: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "l" 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: "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: 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: "E" 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: "F" 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: "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: "C" 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 Time building chain proxies: 3.63, per 1000 atoms: 0.23 Number of scatterers: 15679 At special positions: 0 Unit cell: (128.75, 122.57, 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 3204 8.00 N 2618 7.00 C 9758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 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 C 605 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.07 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.07 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 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 K 3 " - " MAN K 4 " " BMA Y 3 " - " MAN Y 4 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA Y 3 " - " MAN Y 5 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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 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 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-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 137 " " NAG B 601 " - " ASN B 133 " " NAG B 602 " - " ASN B 234 " " NAG B 603 " - " ASN B 88 " " NAG B 604 " - " ASN B 137 " " NAG C 701 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 137 " " NAG F 701 " - " ASN F 637 " " NAG G 1 " - " ASN E 156 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 276 " " NAG N 1 " - " ASN E 295 " " NAG O 1 " - " ASN E 301 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN E 392 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 88 " " NAG U 1 " - " ASN F 611 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 197 " " NAG X 1 " - " ASN A 234 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 332 " " NAG c 1 " - " ASN A 386 " " NAG d 1 " - " ASN A 392 " " NAG e 1 " - " ASN A 448 " " NAG f 1 " - " ASN A 88 " " NAG g 1 " - " ASN C 611 " " NAG h 1 " - " ASN C 618 " " NAG i 1 " - " ASN B 156 " " NAG j 1 " - " ASN B 160 " " NAG k 1 " - " ASN B 197 " " NAG l 1 " - " ASN B 262 " " NAG m 1 " - " ASN B 276 " " NAG n 1 " - " ASN B 295 " " NAG o 1 " - " ASN B 301 " " NAG p 1 " - " ASN B 332 " " NAG q 1 " - " ASN B 386 " " NAG r 1 " - " ASN B 392 " " NAG s 1 " - " ASN B 448 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 565.3 milliseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3566 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 41 sheets defined 26.7% alpha, 73.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.176A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.058A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.398A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.511A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.703A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' 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 115 removed outlier: 4.152A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.039A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.818A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 596 removed outlier: 3.531A pdb=" N LYS C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 661 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.200A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.953A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.995A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.923A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 3.735A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 44 through 45 removed outlier: 6.577A pdb=" N UNK H 34 " --> pdb=" O UNK H 94 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N UNK H 112 " --> pdb=" O UNK H 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 50 through 51 removed outlier: 3.551A pdb=" N UNK H 51 " --> pdb=" O UNK H 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 66 through 69 removed outlier: 6.457A pdb=" N UNK H 66 " --> pdb=" O UNK H 78 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N UNK H 78 " --> pdb=" O UNK H 66 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N UNK H 68 " --> pdb=" O UNK H 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.390A pdb=" N UNK L 36 " --> pdb=" O UNK L 48 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N UNK L 97 " --> pdb=" O UNK L 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.498A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.801A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AB2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.168A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.455A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.658A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.455A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.420A pdb=" N VAL C 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL A 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR C 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR A 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N CYS C 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.699A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AC4, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AC5, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.089A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.395A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.389A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.502A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.395A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.389A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.380A pdb=" N VAL D 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR D 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR B 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N CYS D 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.757A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AD6, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AD7, first strand: chain 'B' and resid 169 through 176 Processing sheet with id=AD8, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.208A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.324A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 315 through 323A removed outlier: 6.470A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.620A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.324A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 315 through 323A removed outlier: 6.470A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2619 1.31 - 1.45: 4815 1.45 - 1.59: 8327 1.59 - 1.73: 59 1.73 - 1.87: 127 Bond restraints: 15947 Sorted by residual: bond pdb=" CB ASN A 195 " pdb=" CG ASN A 195 " ideal model delta sigma weight residual 1.516 1.347 0.169 2.50e-02 1.60e+03 4.57e+01 bond pdb=" CB ASN E 195 " pdb=" CG ASN E 195 " ideal model delta sigma weight residual 1.516 1.353 0.163 2.50e-02 1.60e+03 4.24e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" C LYS D 655 " pdb=" O LYS D 655 " ideal model delta sigma weight residual 1.237 1.164 0.073 1.19e-02 7.06e+03 3.71e+01 bond pdb=" NE ARG B 503 " pdb=" CZ ARG B 503 " ideal model delta sigma weight residual 1.326 1.391 -0.065 1.10e-02 8.26e+03 3.44e+01 ... (remaining 15942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 20887 4.03 - 8.05: 760 8.05 - 12.08: 36 12.08 - 16.11: 7 16.11 - 20.13: 2 Bond angle restraints: 21692 Sorted by residual: angle pdb=" N ASP A 141 " pdb=" CA ASP A 141 " pdb=" C ASP A 141 " ideal model delta sigma weight residual 113.88 93.75 20.13 1.23e+00 6.61e-01 2.68e+02 angle pdb=" N LEU D 544 " pdb=" CA LEU D 544 " pdb=" C LEU D 544 " ideal model delta sigma weight residual 110.48 98.59 11.89 1.48e+00 4.57e-01 6.46e+01 angle pdb=" C CYS B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta sigma weight residual 119.56 127.60 -8.04 1.02e+00 9.61e-01 6.22e+01 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 127.22 -7.66 1.02e+00 9.61e-01 5.64e+01 angle pdb=" N SER B 56 " pdb=" CA SER B 56 " pdb=" C SER B 56 " ideal model delta sigma weight residual 113.89 125.65 -11.76 1.58e+00 4.01e-01 5.54e+01 ... (remaining 21687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 8423 15.35 - 30.70: 274 30.70 - 46.05: 60 46.05 - 61.40: 43 61.40 - 76.75: 9 Dihedral angle restraints: 8809 sinusoidal: 3333 harmonic: 5476 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.56 -63.56 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.28 -60.28 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.90 -54.90 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 8806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2121 0.158 - 0.315: 494 0.315 - 0.473: 166 0.473 - 0.631: 8 0.631 - 0.789: 1 Chirality restraints: 2790 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-02 2.50e+03 1.55e+03 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.69e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.84e+02 ... (remaining 2787 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " 0.342 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG j 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.338 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG h 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 1 " 0.314 2.00e-02 2.50e+03 2.73e-01 9.34e+02 pdb=" C7 NAG h 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG h 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG h 1 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG h 1 " 0.200 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 155 2.62 - 3.19: 13566 3.19 - 3.76: 21981 3.76 - 4.33: 33196 4.33 - 4.90: 51310 Nonbonded interactions: 120208 Sorted by model distance: nonbonded pdb=" O3 NAG A 605 " pdb=" O7 NAG A 605 " model vdw 2.051 3.040 nonbonded pdb=" O3 NAG g 2 " pdb=" O7 NAG g 2 " model vdw 2.119 3.040 nonbonded pdb=" O3 NAG g 1 " pdb=" O7 NAG g 1 " model vdw 2.266 3.040 nonbonded pdb=" N ASP A 141 " pdb=" N MET A 150 " model vdw 2.279 2.560 nonbonded pdb=" O UNK H 51 " pdb=" O UNK H 54 " model vdw 2.319 3.040 ... (remaining 120203 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 604) selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 519 through 701) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' 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' 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 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = (chain 'H' and resid 20 through 116) selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'Y' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.650 Find NCS groups from input model: 0.520 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.024 0.169 16080 Z= 1.245 Angle : 1.818 20.134 22058 Z= 1.106 Chirality : 0.153 0.789 2790 Planarity : 0.016 0.294 2646 Dihedral : 9.526 76.748 5144 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.06 % 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: 0.80 (0.20), residues: 1635 helix: -0.04 (0.24), residues: 378 sheet: 1.03 (0.22), residues: 474 loop : 0.70 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 166 TYR 0.045 0.007 TYR B 486 PHE 0.024 0.007 PHE B 383 TRP 0.043 0.009 TRP E 35 HIS 0.008 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02323 / 1.22 (15947) covalent geometry : angle 1.76097 / 1.10 (21692) SS BOND : bond 0.01385 / 0.72 ( 33) SS BOND : angle 3.16399 / 1.63 ( 66) hydrogen bonds : bond 0.17231 / 9.33 ( 548) hydrogen bonds : angle 8.04661 / 4.63 ( 1944) link_ALPHA1-3 : bond 0.08162 / 4.09 ( 3) link_ALPHA1-3 : angle 4.26315 / 2.08 ( 9) link_ALPHA1-6 : bond 0.06039 / 3.03 ( 3) link_ALPHA1-6 : angle 3.85801 / 1.85 ( 9) link_BETA1-4 : bond 0.06914 / 3.79 ( 40) link_BETA1-4 : angle 5.13525 / 2.50 ( 120) link_NAG-ASN : bond 0.07068 / 3.82 ( 54) link_NAG-ASN : angle 3.05969 / 1.57 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 579 ARG cc_start: 0.8872 (mtp180) cc_final: 0.8569 (mtm-85) REVERT: A 432 GLN cc_start: 0.8460 (mp10) cc_final: 0.8169 (mp10) REVERT: B 342 LEU cc_start: 0.9450 (tp) cc_final: 0.9208 (tp) REVERT: D 573 ILE cc_start: 0.9047 (tp) cc_final: 0.8769 (tt) REVERT: D 659 ASP cc_start: 0.8383 (m-30) cc_final: 0.7737 (m-30) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1595 time to fit residues: 54.4745 Evaluate side-chains 132 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 130 GLN A 33 ASN A 130 GLN A 302 ASN B 249 HIS D 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.056955 restraints weight = 47449.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.058985 restraints weight = 23986.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060338 restraints weight = 15923.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.061181 restraints weight = 12291.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.061787 restraints weight = 10419.431| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16080 Z= 0.159 Angle : 0.754 13.159 22058 Z= 0.360 Chirality : 0.046 0.395 2790 Planarity : 0.004 0.036 2646 Dihedral : 4.811 22.337 1979 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.74 % Allowed : 5.02 % Favored : 94.24 % 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: 1.24 (0.21), residues: 1635 helix: 1.53 (0.28), residues: 384 sheet: 1.01 (0.24), residues: 408 loop : 0.52 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 617 TYR 0.020 0.001 TYR A 217 PHE 0.017 0.002 PHE C 522 TRP 0.025 0.002 TRP D 571 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (15947) covalent geometry : angle 0.70290 / 0.35 (21692) SS BOND : bond 0.00242 / 0.13 ( 33) SS BOND : angle 0.71876 / 0.37 ( 66) hydrogen bonds : bond 0.06068 / 3.30 ( 548) hydrogen bonds : angle 5.54720 / 3.13 ( 1944) link_ALPHA1-3 : bond 0.00725 / 0.36 ( 3) link_ALPHA1-3 : angle 1.39797 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00537 / 0.27 ( 3) link_ALPHA1-6 : angle 1.57081 / 0.84 ( 9) link_BETA1-4 : bond 0.00642 / 0.34 ( 40) link_BETA1-4 : angle 2.60052 / 1.26 ( 120) link_NAG-ASN : bond 0.00407 / 0.23 ( 54) link_NAG-ASN : angle 2.42308 / 1.21 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: F 588 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8395 (ttm110) REVERT: C 530 MET cc_start: 0.8690 (mtp) cc_final: 0.8167 (mtp) REVERT: C 542 ARG cc_start: 0.8813 (ttp-110) cc_final: 0.8598 (ttp-110) REVERT: C 657 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8041 (pt0) REVERT: D 617 ARG cc_start: 0.9069 (mtp85) cc_final: 0.8822 (mmm-85) REVERT: D 653 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8160 (tm-30) REVERT: D 659 ASP cc_start: 0.8512 (m-30) cc_final: 0.8080 (m-30) outliers start: 11 outliers final: 3 residues processed: 187 average time/residue: 0.1204 time to fit residues: 33.5537 Evaluate side-chains 139 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 103 GLN A 33 ASN A 99 ASN A 170 GLN A 302 ASN D 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.056323 restraints weight = 47618.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058369 restraints weight = 23985.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.059721 restraints weight = 15867.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060620 restraints weight = 12220.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.061178 restraints weight = 10268.776| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16080 Z= 0.135 Angle : 0.622 10.926 22058 Z= 0.297 Chirality : 0.043 0.385 2790 Planarity : 0.004 0.061 2646 Dihedral : 4.365 17.636 1979 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.87 % Allowed : 6.16 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1635 helix: 1.78 (0.28), residues: 384 sheet: 0.79 (0.24), residues: 456 loop : 0.38 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 617 TYR 0.017 0.001 TYR A 217 PHE 0.011 0.001 PHE B 53 TRP 0.015 0.001 TRP D 571 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15947) covalent geometry : angle 0.58623 / 0.29 (21692) SS BOND : bond 0.00215 / 0.12 ( 33) SS BOND : angle 0.44696 / 0.23 ( 66) hydrogen bonds : bond 0.04744 / 2.58 ( 548) hydrogen bonds : angle 4.86205 / 2.74 ( 1944) link_ALPHA1-3 : bond 0.00712 / 0.35 ( 3) link_ALPHA1-3 : angle 1.35476 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00637 / 0.32 ( 3) link_ALPHA1-6 : angle 1.45169 / 0.75 ( 9) link_BETA1-4 : bond 0.00597 / 0.32 ( 40) link_BETA1-4 : angle 1.87462 / 0.89 ( 120) link_NAG-ASN : bond 0.00278 / 0.16 ( 54) link_NAG-ASN : angle 1.94239 / 0.98 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: F 579 ARG cc_start: 0.9155 (mtm-85) cc_final: 0.8884 (mtp180) REVERT: F 588 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8391 (ttm110) REVERT: C 530 MET cc_start: 0.8984 (mtp) cc_final: 0.8505 (mtp) REVERT: C 535 MET cc_start: 0.8793 (mpp) cc_final: 0.7888 (mtm) REVERT: C 622 ILE cc_start: 0.9317 (mt) cc_final: 0.8823 (tp) REVERT: C 654 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7641 (mm-30) REVERT: C 657 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8054 (pt0) REVERT: D 543 ASN cc_start: 0.8730 (m-40) cc_final: 0.8529 (m110) REVERT: D 584 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8538 (mt-10) REVERT: D 617 ARG cc_start: 0.9162 (mtp85) cc_final: 0.8958 (mtp85) REVERT: D 647 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: D 653 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 659 ASP cc_start: 0.8404 (m-30) cc_final: 0.7964 (m-30) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.1319 time to fit residues: 30.9203 Evaluate side-chains 135 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 125 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 ASN A 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056645 restraints weight = 47844.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.058690 restraints weight = 24210.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.060046 restraints weight = 15984.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.060962 restraints weight = 12275.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.061560 restraints weight = 10270.407| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16080 Z= 0.111 Angle : 0.572 10.277 22058 Z= 0.271 Chirality : 0.042 0.325 2790 Planarity : 0.003 0.047 2646 Dihedral : 4.069 15.823 1979 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.87 % Allowed : 7.16 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1635 helix: 1.96 (0.28), residues: 384 sheet: 0.77 (0.24), residues: 456 loop : 0.30 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 588 TYR 0.015 0.001 TYR C 586 PHE 0.011 0.001 PHE B 53 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15947) covalent geometry : angle 0.54156 / 0.27 (21692) SS BOND : bond 0.00181 / 0.10 ( 33) SS BOND : angle 0.37628 / 0.19 ( 66) hydrogen bonds : bond 0.04125 / 2.25 ( 548) hydrogen bonds : angle 4.40657 / 2.48 ( 1944) link_ALPHA1-3 : bond 0.00628 / 0.31 ( 3) link_ALPHA1-3 : angle 1.34216 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00553 / 0.28 ( 3) link_ALPHA1-6 : angle 1.47562 / 0.77 ( 9) link_BETA1-4 : bond 0.00493 / 0.26 ( 40) link_BETA1-4 : angle 1.61692 / 0.78 ( 120) link_NAG-ASN : bond 0.00242 / 0.13 ( 54) link_NAG-ASN : angle 1.73143 / 0.87 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 588 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8368 (ttm110) REVERT: F 622 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.9027 (tt) REVERT: F 653 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 195 ASN cc_start: 0.7853 (p0) cc_final: 0.7376 (p0) REVERT: C 530 MET cc_start: 0.9037 (mtp) cc_final: 0.8625 (mtp) REVERT: C 584 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8505 (mt-10) REVERT: C 622 ILE cc_start: 0.9362 (mt) cc_final: 0.9068 (tp) REVERT: D 618 ASN cc_start: 0.7515 (m-40) cc_final: 0.7242 (m-40) REVERT: D 621 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8283 (pm20) REVERT: D 659 ASP cc_start: 0.8339 (m-30) cc_final: 0.7913 (m-30) outliers start: 13 outliers final: 8 residues processed: 160 average time/residue: 0.1313 time to fit residues: 30.9741 Evaluate side-chains 144 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 19 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 328 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN C 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054414 restraints weight = 48179.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.056392 restraints weight = 24795.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.057712 restraints weight = 16529.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.058606 restraints weight = 12771.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.059181 restraints weight = 10753.699| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16080 Z= 0.166 Angle : 0.595 9.805 22058 Z= 0.282 Chirality : 0.043 0.319 2790 Planarity : 0.003 0.046 2646 Dihedral : 3.981 15.083 1979 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.00 % Allowed : 7.43 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1635 helix: 2.52 (0.29), residues: 348 sheet: 0.99 (0.24), residues: 435 loop : 0.24 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 298 TYR 0.022 0.001 TYR D 586 PHE 0.011 0.002 PHE A 361 TRP 0.014 0.001 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15947) covalent geometry : angle 0.56706 / 0.28 (21692) SS BOND : bond 0.00229 / 0.12 ( 33) SS BOND : angle 0.46628 / 0.23 ( 66) hydrogen bonds : bond 0.04227 / 2.31 ( 548) hydrogen bonds : angle 4.31974 / 2.41 ( 1944) link_ALPHA1-3 : bond 0.00652 / 0.32 ( 3) link_ALPHA1-3 : angle 1.35942 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00467 / 0.23 ( 3) link_ALPHA1-6 : angle 1.51161 / 0.80 ( 9) link_BETA1-4 : bond 0.00455 / 0.24 ( 40) link_BETA1-4 : angle 1.59083 / 0.76 ( 120) link_NAG-ASN : bond 0.00261 / 0.15 ( 54) link_NAG-ASN : angle 1.71249 / 0.86 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: C 530 MET cc_start: 0.9104 (mtp) cc_final: 0.8576 (mtp) REVERT: C 584 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8322 (mt-10) REVERT: C 622 ILE cc_start: 0.9330 (mt) cc_final: 0.9116 (mm) REVERT: D 584 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8547 (mt-10) REVERT: D 586 TYR cc_start: 0.9300 (t80) cc_final: 0.9042 (t80) REVERT: D 621 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8423 (pt0) REVERT: D 633 LYS cc_start: 0.9397 (mptt) cc_final: 0.9126 (mmtm) outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 0.1281 time to fit residues: 27.5200 Evaluate side-chains 135 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 118 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.053596 restraints weight = 48543.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.055537 restraints weight = 25014.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.056854 restraints weight = 16719.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.057734 restraints weight = 12947.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058268 restraints weight = 10897.714| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16080 Z= 0.199 Angle : 0.612 11.383 22058 Z= 0.289 Chirality : 0.043 0.309 2790 Planarity : 0.003 0.049 2646 Dihedral : 4.019 15.041 1979 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.07 % Allowed : 7.36 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1635 helix: 2.51 (0.28), residues: 348 sheet: 1.05 (0.25), residues: 399 loop : 0.08 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 588 TYR 0.016 0.001 TYR D 586 PHE 0.013 0.001 PHE A 361 TRP 0.013 0.001 TRP D 571 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (15947) covalent geometry : angle 0.58626 / 0.28 (21692) SS BOND : bond 0.00270 / 0.15 ( 33) SS BOND : angle 0.44869 / 0.22 ( 66) hydrogen bonds : bond 0.04272 / 2.33 ( 548) hydrogen bonds : angle 4.27636 / 2.40 ( 1944) link_ALPHA1-3 : bond 0.00702 / 0.35 ( 3) link_ALPHA1-3 : angle 1.37100 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00408 / 0.20 ( 3) link_ALPHA1-6 : angle 1.53372 / 0.82 ( 9) link_BETA1-4 : bond 0.00432 / 0.23 ( 40) link_BETA1-4 : angle 1.54765 / 0.74 ( 120) link_NAG-ASN : bond 0.00311 / 0.17 ( 54) link_NAG-ASN : angle 1.72026 / 0.87 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: C 584 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8331 (mt-10) REVERT: D 584 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8527 (mt-10) REVERT: D 586 TYR cc_start: 0.9367 (t80) cc_final: 0.9096 (t80) REVERT: D 621 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8341 (pm20) REVERT: D 633 LYS cc_start: 0.9432 (mptt) cc_final: 0.9198 (mmmm) REVERT: D 659 ASP cc_start: 0.8380 (m-30) cc_final: 0.8168 (m-30) outliers start: 16 outliers final: 11 residues processed: 139 average time/residue: 0.1309 time to fit residues: 27.0473 Evaluate side-chains 131 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 165 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.054475 restraints weight = 48064.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.056462 restraints weight = 24654.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.057792 restraints weight = 16394.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.058674 restraints weight = 12655.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.059243 restraints weight = 10653.080| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16080 Z= 0.124 Angle : 0.563 11.817 22058 Z= 0.266 Chirality : 0.042 0.310 2790 Planarity : 0.003 0.047 2646 Dihedral : 3.922 15.828 1979 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 7.76 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1635 helix: 2.27 (0.28), residues: 366 sheet: 0.89 (0.24), residues: 435 loop : 0.15 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 588 TYR 0.015 0.001 TYR D 586 PHE 0.010 0.001 PHE A 53 TRP 0.012 0.001 TRP D 571 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15947) covalent geometry : angle 0.53807 / 0.26 (21692) SS BOND : bond 0.00191 / 0.11 ( 33) SS BOND : angle 0.37673 / 0.19 ( 66) hydrogen bonds : bond 0.03954 / 2.17 ( 548) hydrogen bonds : angle 4.09373 / 2.29 ( 1944) link_ALPHA1-3 : bond 0.00657 / 0.33 ( 3) link_ALPHA1-3 : angle 1.33588 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00432 / 0.22 ( 3) link_ALPHA1-6 : angle 1.50600 / 0.80 ( 9) link_BETA1-4 : bond 0.00466 / 0.25 ( 40) link_BETA1-4 : angle 1.45767 / 0.70 ( 120) link_NAG-ASN : bond 0.00201 / 0.11 ( 54) link_NAG-ASN : angle 1.57621 / 0.80 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8618 (mt-10) REVERT: C 530 MET cc_start: 0.9095 (mtp) cc_final: 0.8641 (mtp) REVERT: C 584 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8364 (mt-10) REVERT: D 584 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8485 (mt-10) REVERT: D 586 TYR cc_start: 0.9348 (t80) cc_final: 0.9061 (t80) REVERT: D 621 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8175 (mp0) REVERT: D 633 LYS cc_start: 0.9427 (mptt) cc_final: 0.9192 (mmmm) outliers start: 13 outliers final: 11 residues processed: 136 average time/residue: 0.1216 time to fit residues: 25.0425 Evaluate side-chains 134 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 74 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 0.0020 chunk 112 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 overall best weight: 0.5448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** A 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 = 0.3123 r_free = 0.3123 target = 0.070699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.055454 restraints weight = 48119.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.057460 restraints weight = 24559.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.058820 restraints weight = 16269.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.059710 restraints weight = 12496.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060258 restraints weight = 10481.490| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16080 Z= 0.100 Angle : 0.537 12.061 22058 Z= 0.253 Chirality : 0.042 0.305 2790 Planarity : 0.003 0.045 2646 Dihedral : 3.759 16.433 1979 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.00 % Allowed : 7.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1635 helix: 2.06 (0.28), residues: 384 sheet: 1.03 (0.25), residues: 414 loop : 0.16 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 588 TYR 0.021 0.001 TYR F 586 PHE 0.011 0.001 PHE A 53 TRP 0.025 0.001 TRP A 479 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (15947) covalent geometry : angle 0.51445 / 0.25 (21692) SS BOND : bond 0.00162 / 0.09 ( 33) SS BOND : angle 0.33918 / 0.17 ( 66) hydrogen bonds : bond 0.03588 / 1.97 ( 548) hydrogen bonds : angle 3.92053 / 2.19 ( 1944) link_ALPHA1-3 : bond 0.00637 / 0.32 ( 3) link_ALPHA1-3 : angle 1.33945 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00434 / 0.22 ( 3) link_ALPHA1-6 : angle 1.47373 / 0.79 ( 9) link_BETA1-4 : bond 0.00477 / 0.25 ( 40) link_BETA1-4 : angle 1.39173 / 0.67 ( 120) link_NAG-ASN : bond 0.00190 / 0.11 ( 54) link_NAG-ASN : angle 1.45285 / 0.74 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8549 (mt-10) REVERT: A 50 THR cc_start: 0.9178 (t) cc_final: 0.8957 (m) REVERT: A 195 ASN cc_start: 0.7795 (p0) cc_final: 0.7406 (p0) REVERT: C 530 MET cc_start: 0.9077 (mtp) cc_final: 0.8646 (mtp) REVERT: C 584 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 586 TYR cc_start: 0.9412 (t80) cc_final: 0.9037 (t80) REVERT: D 584 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8461 (mt-10) REVERT: D 621 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8327 (pm20) REVERT: D 633 LYS cc_start: 0.9413 (mptt) cc_final: 0.9185 (mmmm) outliers start: 15 outliers final: 10 residues processed: 142 average time/residue: 0.1287 time to fit residues: 27.3247 Evaluate side-chains 137 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.0050 chunk 100 optimal weight: 2.9990 chunk 179 optimal weight: 0.0020 chunk 2 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.9606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055613 restraints weight = 48092.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.057624 restraints weight = 24752.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.058965 restraints weight = 16481.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.059852 restraints weight = 12718.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060438 restraints weight = 10711.920| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16080 Z= 0.125 Angle : 0.551 12.512 22058 Z= 0.260 Chirality : 0.042 0.288 2790 Planarity : 0.003 0.051 2646 Dihedral : 3.735 15.138 1979 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.80 % Allowed : 8.37 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.21), residues: 1635 helix: 2.43 (0.29), residues: 366 sheet: 1.18 (0.26), residues: 384 loop : 0.10 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 588 TYR 0.032 0.001 TYR F 586 PHE 0.010 0.001 PHE A 53 TRP 0.010 0.001 TRP A 479 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (15947) covalent geometry : angle 0.52921 / 0.26 (21692) SS BOND : bond 0.00187 / 0.10 ( 33) SS BOND : angle 0.36470 / 0.18 ( 66) hydrogen bonds : bond 0.03665 / 2.01 ( 548) hydrogen bonds : angle 3.92510 / 2.19 ( 1944) link_ALPHA1-3 : bond 0.00629 / 0.31 ( 3) link_ALPHA1-3 : angle 1.35128 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00408 / 0.20 ( 3) link_ALPHA1-6 : angle 1.49299 / 0.80 ( 9) link_BETA1-4 : bond 0.00447 / 0.24 ( 40) link_BETA1-4 : angle 1.41138 / 0.68 ( 120) link_NAG-ASN : bond 0.00190 / 0.11 ( 54) link_NAG-ASN : angle 1.46504 / 0.74 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8574 (mt-10) REVERT: A 50 THR cc_start: 0.9188 (t) cc_final: 0.8958 (m) REVERT: C 530 MET cc_start: 0.9072 (mtp) cc_final: 0.8615 (mtp) REVERT: C 584 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8416 (mt-10) REVERT: C 586 TYR cc_start: 0.9445 (t80) cc_final: 0.9105 (t80) REVERT: D 530 MET cc_start: 0.9095 (mmm) cc_final: 0.8655 (mtp) REVERT: D 584 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8423 (mt-10) REVERT: D 621 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8145 (mp0) REVERT: D 633 LYS cc_start: 0.9389 (mptt) cc_final: 0.9170 (mmmm) REVERT: D 655 LYS cc_start: 0.8918 (tptp) cc_final: 0.8663 (tptp) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 0.1225 time to fit residues: 24.7207 Evaluate side-chains 137 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 112 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN B 302 ASN D 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.054268 restraints weight = 48351.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.056249 restraints weight = 24978.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.057569 restraints weight = 16680.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.058433 restraints weight = 12896.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059013 restraints weight = 10883.484| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16080 Z= 0.171 Angle : 0.592 12.927 22058 Z= 0.278 Chirality : 0.043 0.289 2790 Planarity : 0.004 0.052 2646 Dihedral : 3.874 16.294 1979 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.87 % Allowed : 8.50 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1635 helix: 2.48 (0.29), residues: 366 sheet: 1.11 (0.26), residues: 384 loop : 0.04 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 588 TYR 0.033 0.001 TYR F 586 PHE 0.011 0.001 PHE C 522 TRP 0.008 0.001 TRP A 96 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (15947) covalent geometry : angle 0.56887 / 0.27 (21692) SS BOND : bond 0.00245 / 0.13 ( 33) SS BOND : angle 0.41217 / 0.21 ( 66) hydrogen bonds : bond 0.04056 / 2.22 ( 548) hydrogen bonds : angle 4.06351 / 2.27 ( 1944) link_ALPHA1-3 : bond 0.00630 / 0.31 ( 3) link_ALPHA1-3 : angle 1.35251 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00347 / 0.17 ( 3) link_ALPHA1-6 : angle 1.54656 / 0.83 ( 9) link_BETA1-4 : bond 0.00409 / 0.22 ( 40) link_BETA1-4 : angle 1.45411 / 0.70 ( 120) link_NAG-ASN : bond 0.00278 / 0.15 ( 54) link_NAG-ASN : angle 1.56098 / 0.79 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8588 (mt-10) REVERT: C 530 MET cc_start: 0.9101 (mtp) cc_final: 0.8690 (mtp) REVERT: C 584 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8344 (mt-10) REVERT: D 530 MET cc_start: 0.9028 (mmm) cc_final: 0.8561 (mtp) REVERT: D 584 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8468 (mt-10) REVERT: D 586 TYR cc_start: 0.9286 (t80) cc_final: 0.9061 (t80) REVERT: D 633 LYS cc_start: 0.9393 (mptt) cc_final: 0.9186 (mmmm) REVERT: D 655 LYS cc_start: 0.8930 (tptp) cc_final: 0.8653 (tptp) outliers start: 13 outliers final: 11 residues processed: 135 average time/residue: 0.1207 time to fit residues: 24.6047 Evaluate side-chains 135 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 89 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN D 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.054224 restraints weight = 48094.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.056194 restraints weight = 25065.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.057501 restraints weight = 16875.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.058311 restraints weight = 13117.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.058886 restraints weight = 11175.049| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 16080 Z= 0.205 Angle : 0.783 59.189 22058 Z= 0.427 Chirality : 0.046 0.981 2790 Planarity : 0.004 0.057 2646 Dihedral : 3.919 25.205 1979 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.80 % Allowed : 8.77 % Favored : 90.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1635 helix: 2.47 (0.29), residues: 366 sheet: 1.11 (0.26), residues: 384 loop : 0.03 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 588 TYR 0.025 0.001 TYR F 586 PHE 0.011 0.001 PHE C 522 TRP 0.008 0.001 TRP A 96 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (15947) covalent geometry : angle 0.76864 / 0.43 (21692) SS BOND : bond 0.00228 / 0.12 ( 33) SS BOND : angle 0.41118 / 0.21 ( 66) hydrogen bonds : bond 0.04037 / 2.21 ( 548) hydrogen bonds : angle 4.06302 / 2.27 ( 1944) link_ALPHA1-3 : bond 0.00631 / 0.31 ( 3) link_ALPHA1-3 : angle 1.35146 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00351 / 0.18 ( 3) link_ALPHA1-6 : angle 1.55380 / 0.84 ( 9) link_BETA1-4 : bond 0.00390 / 0.21 ( 40) link_BETA1-4 : angle 1.45300 / 0.70 ( 120) link_NAG-ASN : bond 0.00273 / 0.15 ( 54) link_NAG-ASN : angle 1.56277 / 0.79 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2108.29 seconds wall clock time: 37 minutes 36.10 seconds (2256.10 seconds total)