Starting phenix.real_space_refine on Wed Mar 4 19:52:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8a_23227/03_2026/7l8a_23227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8a_23227/03_2026/7l8a_23227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l8a_23227/03_2026/7l8a_23227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8a_23227/03_2026/7l8a_23227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8a_23227/03_2026/7l8a_23227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8a_23227/03_2026/7l8a_23227.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9783 2.51 5 N 2635 2.21 5 O 3211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15728 Number of models: 1 Model: "" Number of chains: 47 Chain: "E" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3460 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 948 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3480 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.95, per 1000 atoms: 0.25 Number of scatterers: 15728 At special positions: 0 Unit cell: (151.41, 126.69, 118.45, 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 3211 8.00 N 2635 7.00 C 9783 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=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.08 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.11 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS 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 W 3 " - " MAN W 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA W 3 " - " MAN W 5 " " BMA h 3 " - " MAN h 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 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 A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 398 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 137 " " 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 392 " " NAG E 604 " - " ASN E 137 " " NAG E 605 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " 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 448 " " NAG S 1 " - " ASN E 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 295 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 448 " " NAG d 1 " - " ASN A 88 " " NAG e 1 " - " ASN C 156 " " NAG f 1 " - " ASN C 197 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 262 " " NAG i 1 " - " ASN C 276 " " NAG j 1 " - " ASN C 301 " " NAG k 1 " - " ASN C 332 " " NAG l 1 " - " ASN C 386 " " NAG m 1 " - " ASN C 392 " " NAG n 1 " - " ASN C 448 " " NAG o 1 " - " ASN C 88 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 651.1 milliseconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 35 sheets defined 26.7% alpha, 51.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.127A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.968A 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: 4.422A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.839A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.759A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 69 removed outlier: 5.551A pdb=" N UNK H 67 " --> pdb=" O UNK H 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.096A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.607A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.890A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.023A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.806A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.675A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.517A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 544 removed outlier: 4.192A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.885A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.482A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.852A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.062A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.445A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.601A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.601A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.709A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.601A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.709A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.462A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.822A pdb=" N UNK H 37 " --> pdb=" O UNK H 49 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N UNK H 51 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N UNK H 35 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N UNK H 34 " --> pdb=" O UNK H 100 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N UNK H 106 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.822A pdb=" N UNK H 37 " --> pdb=" O UNK H 49 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N UNK H 51 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N UNK H 35 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N UNK H 34 " --> pdb=" O UNK H 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.213A pdb=" N UNK L 22 " --> pdb=" O UNK L 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.949A pdb=" N UNK L 11 " --> pdb=" O UNK L 105 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.485A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.777A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.518A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.658A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.658A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.071A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.706A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.658A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.071A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.706A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.551A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.322A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.900A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.067A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD4, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.939A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.615A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.615A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.036A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.733A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.615A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.036A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.733A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.762A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1698 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: 2.91 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3338 1.32 - 1.46: 5023 1.46 - 1.59: 7482 1.59 - 1.73: 24 1.73 - 1.87: 129 Bond restraints: 15996 Sorted by residual: bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.632 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" CB HIS A 352 " pdb=" CG HIS A 352 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" CB ASN A 478 " pdb=" CG ASN A 478 " ideal model delta sigma weight residual 1.516 1.396 0.120 2.50e-02 1.60e+03 2.31e+01 bond pdb=" NE1 TRP E 427 " pdb=" CE2 TRP E 427 " ideal model delta sigma weight residual 1.370 1.319 0.051 1.10e-02 8.26e+03 2.17e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.319 0.051 1.10e-02 8.26e+03 2.17e+01 ... (remaining 15991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 18385 2.24 - 4.48: 2866 4.48 - 6.73: 450 6.73 - 8.97: 55 8.97 - 11.21: 8 Bond angle restraints: 21764 Sorted by residual: angle pdb=" C CYS E 239 " pdb=" N PRO E 240 " pdb=" CA PRO E 240 " ideal model delta sigma weight residual 119.56 127.56 -8.00 1.02e+00 9.61e-01 6.16e+01 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 99.27 11.21 1.48e+00 4.57e-01 5.74e+01 angle pdb=" N THR A 461 " pdb=" CA THR A 461 " pdb=" C THR A 461 " ideal model delta sigma weight residual 114.56 105.04 9.52 1.27e+00 6.20e-01 5.62e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 126.87 -7.31 1.01e+00 9.80e-01 5.24e+01 angle pdb=" N GLU E 87 " pdb=" CA GLU E 87 " pdb=" C GLU E 87 " ideal model delta sigma weight residual 111.28 119.11 -7.83 1.09e+00 8.42e-01 5.16e+01 ... (remaining 21759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 10579 21.86 - 43.72: 208 43.72 - 65.58: 56 65.58 - 87.43: 30 87.43 - 109.29: 14 Dihedral angle restraints: 10887 sinusoidal: 5357 harmonic: 5530 Sorted by residual: 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 93.00 159.69 -66.69 1 1.00e+01 1.00e-02 5.80e+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 93.00 152.20 -59.20 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.81 41.81 1 1.00e+01 1.00e-02 2.44e+01 ... (remaining 10884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1764 0.099 - 0.198: 548 0.198 - 0.298: 277 0.298 - 0.397: 123 0.397 - 0.496: 82 Chirality restraints: 2794 Sorted by residual: chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.60e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.53e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.50e+02 ... (remaining 2791 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.286 2.00e-02 2.50e+03 2.46e-01 7.55e+02 pdb=" C7 NAG d 1 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.419 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 702 " -0.182 2.00e-02 2.50e+03 1.54e-01 2.98e+02 pdb=" C7 NAG D 702 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG D 702 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG D 702 " 0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 702 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " -0.156 2.00e-02 2.50e+03 1.29e-01 2.08e+02 pdb=" C7 NAG F 702 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.115 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " 0.209 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " 0.019 2.00e-02 2.50e+03 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1993 2.74 - 3.28: 14303 3.28 - 3.82: 23995 3.82 - 4.36: 30989 4.36 - 4.90: 49778 Nonbonded interactions: 121058 Sorted by model distance: nonbonded pdb=" OG SER D 528 " pdb=" O7 NAG o 1 " model vdw 2.195 3.040 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.378 3.120 nonbonded pdb=" N LEU B 544 " pdb=" O LEU B 544 " model vdw 2.398 2.496 nonbonded pdb=" N UNK L 50 " pdb=" O UNK L 50 " model vdw 2.401 2.496 nonbonded pdb=" N THR A 461 " pdb=" N ASN A 462 " model vdw 2.408 2.560 ... (remaining 121053 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 57 or resid 66 through 397 or resid 410 through \ 605)) selection = (chain 'C' and (resid 33 through 184 or resid 189 through 605)) selection = (chain 'E' and (resid 33 through 57 or resid 66 through 184 or resid 189 through \ 605)) } ncs_group { reference = (chain 'B' and (resid 519 through 546 or resid 572 through 702)) selection = (chain 'D' and (resid 519 through 546 or resid 572 through 702)) 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 'X' selection = chain 'Y' 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 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } ncs_group { reference = (chain 'H' and resid 11 through 115) selection = chain 'L' } ncs_group { reference = chain 'W' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 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: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.270 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 0.148 16126 Z= 1.244 Angle : 1.737 11.209 22121 Z= 1.084 Chirality : 0.150 0.496 2794 Planarity : 0.010 0.246 2664 Dihedral : 10.984 109.293 7190 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.68 (0.19), residues: 1651 helix: -0.18 (0.23), residues: 418 sheet: 1.18 (0.23), residues: 432 loop : 0.57 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 166 TYR 0.049 0.007 TYR A 191 PHE 0.028 0.005 PHE A 383 TRP 0.054 0.009 TRP C 69 HIS 0.017 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.02317 (15996) covalent geometry : angle 1.69171 (21764) SS BOND : bond 0.02033 ( 33) SS BOND : angle 2.84785 ( 66) hydrogen bonds : bond 0.16375 ( 591) hydrogen bonds : angle 7.22930 ( 1698) link_ALPHA1-3 : bond 0.08154 ( 3) link_ALPHA1-3 : angle 4.36822 ( 9) link_ALPHA1-6 : bond 0.05686 ( 2) link_ALPHA1-6 : angle 3.30889 ( 6) link_BETA1-4 : bond 0.07228 ( 36) link_BETA1-4 : angle 4.83989 ( 108) link_NAG-ASN : bond 0.07134 ( 56) link_NAG-ASN : angle 2.63854 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.456 Fit side-chains REVERT: E 142 MET cc_start: 0.8659 (mmm) cc_final: 0.8398 (mmm) REVERT: E 232 LYS cc_start: 0.7902 (mttt) cc_final: 0.7563 (mtmm) REVERT: A 142 MET cc_start: 0.8690 (mmm) cc_final: 0.8307 (mmm) REVERT: A 173 TYR cc_start: 0.7778 (p90) cc_final: 0.7518 (m-80) REVERT: B 542 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8247 (mtt90) REVERT: B 579 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8569 (mtp180) REVERT: B 627 THR cc_start: 0.9065 (p) cc_final: 0.8768 (p) REVERT: C 95 MET cc_start: 0.9158 (ptm) cc_final: 0.8937 (ptp) REVERT: D 624 ASP cc_start: 0.8492 (m-30) cc_final: 0.8282 (m-30) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1496 time to fit residues: 71.4089 Evaluate side-chains 164 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN E 246 GLN F 591 GLN A 440 GLN B 570 HIS B 607 ASN C 99 ASN D 607 ASN D 625 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104679 restraints weight = 23185.035| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.54 r_work: 0.3044 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16126 Z= 0.161 Angle : 0.706 7.367 22121 Z= 0.347 Chirality : 0.047 0.315 2794 Planarity : 0.004 0.046 2664 Dihedral : 8.184 83.476 4022 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.27 % Allowed : 6.47 % Favored : 92.26 % 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: 1.06 (0.20), residues: 1651 helix: 1.42 (0.27), residues: 405 sheet: 1.12 (0.24), residues: 430 loop : 0.20 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 542 TYR 0.016 0.001 TYR E 177 PHE 0.016 0.002 PHE E 383 TRP 0.012 0.001 TRP B 571 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00356 (15996) covalent geometry : angle 0.64929 (21764) SS BOND : bond 0.00297 ( 33) SS BOND : angle 1.50164 ( 66) hydrogen bonds : bond 0.05665 ( 591) hydrogen bonds : angle 5.40942 ( 1698) link_ALPHA1-3 : bond 0.01241 ( 3) link_ALPHA1-3 : angle 2.43984 ( 9) link_ALPHA1-6 : bond 0.00832 ( 2) link_ALPHA1-6 : angle 1.75839 ( 6) link_BETA1-4 : bond 0.00468 ( 36) link_BETA1-4 : angle 2.49140 ( 108) link_NAG-ASN : bond 0.00420 ( 56) link_NAG-ASN : angle 2.37729 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 268 GLU cc_start: 0.7282 (pm20) cc_final: 0.7041 (mt-10) REVERT: F 590 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8891 (mm110) REVERT: F 599 SER cc_start: 0.8635 (p) cc_final: 0.8331 (t) REVERT: F 634 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 142 MET cc_start: 0.8536 (mmm) cc_final: 0.8157 (mmm) REVERT: A 173 TYR cc_start: 0.8571 (p90) cc_final: 0.7402 (m-80) REVERT: A 246 GLN cc_start: 0.8144 (tp40) cc_final: 0.7865 (tp40) REVERT: B 542 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8293 (mtt90) REVERT: B 660 LEU cc_start: 0.8685 (mp) cc_final: 0.8355 (mt) REVERT: C 142 MET cc_start: 0.8715 (mmm) cc_final: 0.8372 (mmp) REVERT: C 434 MET cc_start: 0.9278 (ttp) cc_final: 0.9022 (ttt) REVERT: C 464 THR cc_start: 0.8674 (p) cc_final: 0.8282 (t) outliers start: 19 outliers final: 9 residues processed: 251 average time/residue: 0.1206 time to fit residues: 44.6882 Evaluate side-chains 182 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 88 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN C 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104618 restraints weight = 23216.633| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.51 r_work: 0.3052 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16126 Z= 0.143 Angle : 0.631 10.991 22121 Z= 0.311 Chirality : 0.045 0.276 2794 Planarity : 0.003 0.037 2664 Dihedral : 7.360 76.393 4022 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.67 % Allowed : 8.61 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1651 helix: 1.51 (0.27), residues: 407 sheet: 1.15 (0.25), residues: 405 loop : 0.02 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.009 0.001 TYR A 191 PHE 0.012 0.001 PHE C 176 TRP 0.013 0.001 TRP B 571 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00335 (15996) covalent geometry : angle 0.58439 (21764) SS BOND : bond 0.00434 ( 33) SS BOND : angle 2.17609 ( 66) hydrogen bonds : bond 0.04696 ( 591) hydrogen bonds : angle 4.93124 ( 1698) link_ALPHA1-3 : bond 0.01183 ( 3) link_ALPHA1-3 : angle 1.22837 ( 9) link_ALPHA1-6 : bond 0.01107 ( 2) link_ALPHA1-6 : angle 1.95323 ( 6) link_BETA1-4 : bond 0.00529 ( 36) link_BETA1-4 : angle 1.90824 ( 108) link_NAG-ASN : bond 0.00316 ( 56) link_NAG-ASN : angle 1.95190 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: E 502 LYS cc_start: 0.8945 (tmmt) cc_final: 0.8670 (tttp) REVERT: F 599 SER cc_start: 0.8562 (p) cc_final: 0.8268 (t) REVERT: F 634 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 142 MET cc_start: 0.8502 (mmm) cc_final: 0.8065 (mmm) REVERT: A 191 TYR cc_start: 0.9068 (m-80) cc_final: 0.8854 (m-80) REVERT: A 246 GLN cc_start: 0.8165 (tp40) cc_final: 0.7894 (tp40) REVERT: B 542 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8292 (mtt90) REVERT: B 660 LEU cc_start: 0.8645 (mp) cc_final: 0.8263 (mt) REVERT: C 142 MET cc_start: 0.8739 (mmm) cc_final: 0.8407 (mmp) REVERT: C 434 MET cc_start: 0.9319 (ttp) cc_final: 0.9077 (ttt) REVERT: C 464 THR cc_start: 0.8596 (p) cc_final: 0.8224 (t) REVERT: C 475 MET cc_start: 0.8602 (mmt) cc_final: 0.8172 (mmt) outliers start: 25 outliers final: 16 residues processed: 200 average time/residue: 0.1258 time to fit residues: 37.8426 Evaluate side-chains 185 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 127 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 168 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN C 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100379 restraints weight = 23482.299| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.62 r_work: 0.2981 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16126 Z= 0.181 Angle : 0.635 10.639 22121 Z= 0.311 Chirality : 0.046 0.266 2794 Planarity : 0.004 0.040 2664 Dihedral : 6.709 66.125 4022 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.87 % Allowed : 9.21 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1651 helix: 1.50 (0.27), residues: 407 sheet: 0.86 (0.24), residues: 423 loop : -0.20 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 480 TYR 0.012 0.001 TYR C 484 PHE 0.015 0.002 PHE C 53 TRP 0.014 0.001 TRP D 571 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00438 (15996) covalent geometry : angle 0.59728 (21764) SS BOND : bond 0.00507 ( 33) SS BOND : angle 1.71798 ( 66) hydrogen bonds : bond 0.04636 ( 591) hydrogen bonds : angle 4.82463 ( 1698) link_ALPHA1-3 : bond 0.01155 ( 3) link_ALPHA1-3 : angle 1.53036 ( 9) link_ALPHA1-6 : bond 0.01298 ( 2) link_ALPHA1-6 : angle 2.26758 ( 6) link_BETA1-4 : bond 0.00456 ( 36) link_BETA1-4 : angle 1.75036 ( 108) link_NAG-ASN : bond 0.00256 ( 56) link_NAG-ASN : angle 1.87284 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: E 502 LYS cc_start: 0.8917 (tmmt) cc_final: 0.8685 (tttp) REVERT: F 599 SER cc_start: 0.8794 (p) cc_final: 0.8593 (t) REVERT: F 634 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 46 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8609 (mptt) REVERT: A 142 MET cc_start: 0.8653 (mmm) cc_final: 0.8307 (mmm) REVERT: A 246 GLN cc_start: 0.8297 (tp40) cc_final: 0.7992 (tp40) REVERT: B 542 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8356 (mtt90) REVERT: B 632 ASP cc_start: 0.9238 (t0) cc_final: 0.8879 (t0) REVERT: C 434 MET cc_start: 0.9332 (ttp) cc_final: 0.9077 (ttt) REVERT: C 464 THR cc_start: 0.8598 (p) cc_final: 0.8227 (t) REVERT: D 636 SER cc_start: 0.9307 (t) cc_final: 0.9076 (p) REVERT: D 657 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7770 (tp30) outliers start: 28 outliers final: 22 residues processed: 198 average time/residue: 0.1222 time to fit residues: 36.4585 Evaluate side-chains 194 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 69 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097612 restraints weight = 23700.211| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.53 r_work: 0.2942 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 16126 Z= 0.273 Angle : 0.707 10.739 22121 Z= 0.342 Chirality : 0.048 0.292 2794 Planarity : 0.004 0.045 2664 Dihedral : 6.840 60.777 4022 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.27 % Allowed : 10.14 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1651 helix: 1.31 (0.27), residues: 407 sheet: 0.72 (0.25), residues: 397 loop : -0.54 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 480 TYR 0.012 0.002 TYR C 484 PHE 0.016 0.002 PHE E 383 TRP 0.013 0.002 TRP B 571 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00663 (15996) covalent geometry : angle 0.67152 (21764) SS BOND : bond 0.00464 ( 33) SS BOND : angle 1.69523 ( 66) hydrogen bonds : bond 0.05203 ( 591) hydrogen bonds : angle 5.03072 ( 1698) link_ALPHA1-3 : bond 0.01061 ( 3) link_ALPHA1-3 : angle 1.38556 ( 9) link_ALPHA1-6 : bond 0.01134 ( 2) link_ALPHA1-6 : angle 2.25307 ( 6) link_BETA1-4 : bond 0.00453 ( 36) link_BETA1-4 : angle 1.80204 ( 108) link_NAG-ASN : bond 0.00338 ( 56) link_NAG-ASN : angle 1.98815 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 67 ASN cc_start: 0.7625 (p0) cc_final: 0.6900 (m-40) REVERT: E 426 MET cc_start: 0.8630 (mtp) cc_final: 0.8336 (mmm) REVERT: F 634 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 142 MET cc_start: 0.8687 (mmm) cc_final: 0.8456 (mmm) REVERT: A 477 ASP cc_start: 0.9312 (m-30) cc_final: 0.9100 (m-30) REVERT: B 542 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8326 (mtt90) REVERT: C 434 MET cc_start: 0.9357 (ttp) cc_final: 0.9109 (ttt) REVERT: C 464 THR cc_start: 0.8561 (p) cc_final: 0.8179 (t) outliers start: 34 outliers final: 29 residues processed: 192 average time/residue: 0.1193 time to fit residues: 34.6785 Evaluate side-chains 190 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 122 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.100296 restraints weight = 23509.039| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.58 r_work: 0.2956 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16126 Z= 0.156 Angle : 0.595 9.360 22121 Z= 0.291 Chirality : 0.044 0.234 2794 Planarity : 0.004 0.044 2664 Dihedral : 6.340 58.357 4022 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.93 % Allowed : 10.61 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1651 helix: 1.49 (0.27), residues: 408 sheet: 0.69 (0.25), residues: 390 loop : -0.60 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 617 TYR 0.010 0.001 TYR A 191 PHE 0.011 0.001 PHE E 383 TRP 0.013 0.001 TRP D 571 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00369 (15996) covalent geometry : angle 0.55948 (21764) SS BOND : bond 0.00370 ( 33) SS BOND : angle 1.51242 ( 66) hydrogen bonds : bond 0.04350 ( 591) hydrogen bonds : angle 4.73564 ( 1698) link_ALPHA1-3 : bond 0.01058 ( 3) link_ALPHA1-3 : angle 1.36257 ( 9) link_ALPHA1-6 : bond 0.01089 ( 2) link_ALPHA1-6 : angle 1.62281 ( 6) link_BETA1-4 : bond 0.00443 ( 36) link_BETA1-4 : angle 1.60427 ( 108) link_NAG-ASN : bond 0.00267 ( 56) link_NAG-ASN : angle 1.81461 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: E 67 ASN cc_start: 0.7737 (p0) cc_final: 0.7133 (m-40) REVERT: E 153 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8165 (mm-30) REVERT: E 217 TYR cc_start: 0.8943 (m-80) cc_final: 0.8616 (m-80) REVERT: E 426 MET cc_start: 0.8575 (mtp) cc_final: 0.8324 (mmm) REVERT: F 634 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 142 MET cc_start: 0.8640 (mmm) cc_final: 0.8437 (mmm) REVERT: A 477 ASP cc_start: 0.9318 (m-30) cc_final: 0.9097 (m-30) REVERT: B 542 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8301 (mtt90) REVERT: C 205 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6960 (m) REVERT: C 434 MET cc_start: 0.9358 (ttp) cc_final: 0.9102 (ttt) REVERT: C 464 THR cc_start: 0.8575 (p) cc_final: 0.8247 (t) REVERT: D 530 MET cc_start: 0.9073 (mtp) cc_final: 0.8715 (mtp) REVERT: D 657 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7848 (tp30) outliers start: 29 outliers final: 23 residues processed: 188 average time/residue: 0.1244 time to fit residues: 34.8406 Evaluate side-chains 190 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 2.9990 chunk 126 optimal weight: 0.0870 chunk 129 optimal weight: 0.0870 chunk 44 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102665 restraints weight = 23626.644| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.70 r_work: 0.3024 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16126 Z= 0.101 Angle : 0.527 8.315 22121 Z= 0.260 Chirality : 0.042 0.220 2794 Planarity : 0.003 0.040 2664 Dihedral : 5.195 55.402 4022 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.07 % Allowed : 11.61 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1651 helix: 1.63 (0.27), residues: 416 sheet: 0.84 (0.25), residues: 401 loop : -0.58 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.011 0.001 TYR E 191 PHE 0.009 0.001 PHE C 176 TRP 0.011 0.001 TRP D 571 HIS 0.003 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00221 (15996) covalent geometry : angle 0.49401 (21764) SS BOND : bond 0.00324 ( 33) SS BOND : angle 1.36405 ( 66) hydrogen bonds : bond 0.03567 ( 591) hydrogen bonds : angle 4.38884 ( 1698) link_ALPHA1-3 : bond 0.01043 ( 3) link_ALPHA1-3 : angle 1.25556 ( 9) link_ALPHA1-6 : bond 0.01098 ( 2) link_ALPHA1-6 : angle 2.09961 ( 6) link_BETA1-4 : bond 0.00463 ( 36) link_BETA1-4 : angle 1.47021 ( 108) link_NAG-ASN : bond 0.00285 ( 56) link_NAG-ASN : angle 1.62385 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: E 67 ASN cc_start: 0.7629 (p0) cc_final: 0.7067 (m-40) REVERT: E 153 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8295 (mm-30) REVERT: E 217 TYR cc_start: 0.8926 (m-80) cc_final: 0.8616 (m-80) REVERT: E 232 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7882 (mppt) REVERT: E 426 MET cc_start: 0.8631 (mtp) cc_final: 0.8404 (mmm) REVERT: F 634 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 142 MET cc_start: 0.8700 (mmm) cc_final: 0.7878 (mmm) REVERT: A 373 THR cc_start: 0.8824 (m) cc_final: 0.8200 (p) REVERT: A 477 ASP cc_start: 0.9331 (m-30) cc_final: 0.9126 (m-30) REVERT: B 542 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8349 (mtt90) REVERT: C 434 MET cc_start: 0.9290 (ttp) cc_final: 0.9026 (ttt) REVERT: C 464 THR cc_start: 0.8613 (p) cc_final: 0.8325 (t) REVERT: D 530 MET cc_start: 0.9152 (mtp) cc_final: 0.8832 (mtp) outliers start: 16 outliers final: 12 residues processed: 207 average time/residue: 0.1230 time to fit residues: 38.0920 Evaluate side-chains 193 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 165 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098428 restraints weight = 23956.987| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.74 r_work: 0.2951 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16126 Z= 0.210 Angle : 0.642 9.202 22121 Z= 0.313 Chirality : 0.045 0.215 2794 Planarity : 0.004 0.043 2664 Dihedral : 5.502 56.410 4022 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.60 % Allowed : 11.41 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1651 helix: 1.49 (0.27), residues: 409 sheet: 0.69 (0.25), residues: 393 loop : -0.65 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.012 0.001 TYR C 484 PHE 0.014 0.002 PHE E 383 TRP 0.012 0.001 TRP B 571 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00512 (15996) covalent geometry : angle 0.60873 (21764) SS BOND : bond 0.00441 ( 33) SS BOND : angle 1.57436 ( 66) hydrogen bonds : bond 0.04580 ( 591) hydrogen bonds : angle 4.70690 ( 1698) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 1.21059 ( 9) link_ALPHA1-6 : bond 0.00858 ( 2) link_ALPHA1-6 : angle 1.56420 ( 6) link_BETA1-4 : bond 0.00436 ( 36) link_BETA1-4 : angle 1.61627 ( 108) link_NAG-ASN : bond 0.00291 ( 56) link_NAG-ASN : angle 1.83986 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 67 ASN cc_start: 0.7641 (p0) cc_final: 0.7299 (m-40) REVERT: E 153 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8290 (mm-30) REVERT: E 217 TYR cc_start: 0.8930 (m-80) cc_final: 0.8606 (m-80) REVERT: E 426 MET cc_start: 0.8716 (mtp) cc_final: 0.8495 (mmm) REVERT: F 634 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 542 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8360 (mtt90) REVERT: B 616 ASN cc_start: 0.8671 (t0) cc_final: 0.8271 (p0) REVERT: C 434 MET cc_start: 0.9314 (ttp) cc_final: 0.9074 (ttt) REVERT: C 464 THR cc_start: 0.8599 (p) cc_final: 0.8263 (t) outliers start: 24 outliers final: 23 residues processed: 185 average time/residue: 0.1231 time to fit residues: 33.9013 Evaluate side-chains 187 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** C 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 = 0.3391 r_free = 0.3391 target = 0.119451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.098162 restraints weight = 24023.766| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.64 r_work: 0.2907 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16126 Z= 0.269 Angle : 0.704 9.181 22121 Z= 0.342 Chirality : 0.047 0.276 2794 Planarity : 0.004 0.045 2664 Dihedral : 6.009 56.735 4022 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.13 % Allowed : 11.54 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1651 helix: 1.36 (0.27), residues: 403 sheet: 0.45 (0.25), residues: 385 loop : -0.75 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 480 TYR 0.015 0.002 TYR C 191 PHE 0.017 0.002 PHE E 383 TRP 0.016 0.001 TRP B 571 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00656 (15996) covalent geometry : angle 0.66975 (21764) SS BOND : bond 0.00656 ( 33) SS BOND : angle 1.84690 ( 66) hydrogen bonds : bond 0.05112 ( 591) hydrogen bonds : angle 4.96955 ( 1698) link_ALPHA1-3 : bond 0.00894 ( 3) link_ALPHA1-3 : angle 1.17192 ( 9) link_ALPHA1-6 : bond 0.00833 ( 2) link_ALPHA1-6 : angle 1.52803 ( 6) link_BETA1-4 : bond 0.00424 ( 36) link_BETA1-4 : angle 1.69784 ( 108) link_NAG-ASN : bond 0.00361 ( 56) link_NAG-ASN : angle 1.96088 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 153 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 302 ASN cc_start: 0.8961 (m-40) cc_final: 0.8735 (m-40) REVERT: E 426 MET cc_start: 0.8725 (mtp) cc_final: 0.8486 (mmm) REVERT: F 634 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8439 (tm-30) REVERT: A 142 MET cc_start: 0.8540 (mmm) cc_final: 0.8321 (mmm) REVERT: B 542 ARG cc_start: 0.8791 (mtm-85) cc_final: 0.8399 (mtt90) REVERT: B 616 ASN cc_start: 0.8677 (t0) cc_final: 0.8393 (p0) REVERT: C 434 MET cc_start: 0.9333 (ttp) cc_final: 0.9124 (ttt) outliers start: 32 outliers final: 26 residues processed: 180 average time/residue: 0.1229 time to fit residues: 32.9933 Evaluate side-chains 178 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 103 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097281 restraints weight = 23787.785| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.70 r_work: 0.2922 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16126 Z= 0.227 Angle : 0.664 8.816 22121 Z= 0.323 Chirality : 0.046 0.263 2794 Planarity : 0.004 0.046 2664 Dihedral : 6.006 56.509 4022 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.87 % Allowed : 12.01 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1651 helix: 1.41 (0.27), residues: 403 sheet: 0.44 (0.26), residues: 383 loop : -0.78 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 480 TYR 0.012 0.001 TYR C 191 PHE 0.015 0.002 PHE E 383 TRP 0.016 0.001 TRP B 571 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00552 (15996) covalent geometry : angle 0.63010 (21764) SS BOND : bond 0.00492 ( 33) SS BOND : angle 1.69461 ( 66) hydrogen bonds : bond 0.04842 ( 591) hydrogen bonds : angle 4.89193 ( 1698) link_ALPHA1-3 : bond 0.00834 ( 3) link_ALPHA1-3 : angle 1.20675 ( 9) link_ALPHA1-6 : bond 0.00808 ( 2) link_ALPHA1-6 : angle 1.48213 ( 6) link_BETA1-4 : bond 0.00398 ( 36) link_BETA1-4 : angle 1.64859 ( 108) link_NAG-ASN : bond 0.00309 ( 56) link_NAG-ASN : angle 1.89124 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 153 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8341 (mm-30) REVERT: E 217 TYR cc_start: 0.8942 (m-80) cc_final: 0.8636 (m-80) REVERT: E 302 ASN cc_start: 0.8962 (m-40) cc_final: 0.8700 (m-40) REVERT: E 426 MET cc_start: 0.8702 (mtp) cc_final: 0.8470 (mmm) REVERT: F 634 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 142 MET cc_start: 0.8540 (mmm) cc_final: 0.8263 (mmm) REVERT: B 542 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8374 (mtt90) REVERT: B 616 ASN cc_start: 0.8668 (t0) cc_final: 0.8401 (p0) REVERT: B 660 LEU cc_start: 0.8683 (mp) cc_final: 0.8383 (mt) REVERT: C 434 MET cc_start: 0.9339 (ttp) cc_final: 0.9129 (ttt) outliers start: 28 outliers final: 26 residues processed: 175 average time/residue: 0.1290 time to fit residues: 33.5380 Evaluate side-chains 179 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 136 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** C 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 = 0.3424 r_free = 0.3424 target = 0.121239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101318 restraints weight = 24037.725| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.46 r_work: 0.2982 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16126 Z= 0.225 Angle : 0.660 8.688 22121 Z= 0.321 Chirality : 0.046 0.279 2794 Planarity : 0.004 0.046 2664 Dihedral : 6.056 56.641 4022 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.73 % Allowed : 12.14 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1651 helix: 1.44 (0.27), residues: 402 sheet: 0.39 (0.26), residues: 385 loop : -0.81 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 480 TYR 0.012 0.001 TYR C 191 PHE 0.015 0.002 PHE E 383 TRP 0.017 0.001 TRP B 571 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00547 (15996) covalent geometry : angle 0.62595 (21764) SS BOND : bond 0.00484 ( 33) SS BOND : angle 1.67273 ( 66) hydrogen bonds : bond 0.04790 ( 591) hydrogen bonds : angle 4.87706 ( 1698) link_ALPHA1-3 : bond 0.00788 ( 3) link_ALPHA1-3 : angle 1.23274 ( 9) link_ALPHA1-6 : bond 0.00781 ( 2) link_ALPHA1-6 : angle 1.49732 ( 6) link_BETA1-4 : bond 0.00395 ( 36) link_BETA1-4 : angle 1.64757 ( 108) link_NAG-ASN : bond 0.00321 ( 56) link_NAG-ASN : angle 1.88280 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.79 seconds wall clock time: 61 minutes 12.74 seconds (3672.74 seconds total)