Starting phenix.real_space_refine on Sat May 24 20:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u29_41842/05_2025/8u29_41842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u29_41842/05_2025/8u29_41842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u29_41842/05_2025/8u29_41842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u29_41842/05_2025/8u29_41842.map" model { file = "/net/cci-nas-00/data/ceres_data/8u29_41842/05_2025/8u29_41842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u29_41842/05_2025/8u29_41842.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 16434 2.51 5 N 4206 2.21 5 O 4963 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 1.63s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25726 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8073 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 52, 'TRANS': 1029} Chain breaks: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 8075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8075 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 52, 'TRANS': 1029} Chain breaks: 2 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 158 Chain: "C" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8078 Classifications: {'peptide': 1082} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 52, 'TRANS': 1029} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 15, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 155 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: 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: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 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: "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: 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: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 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: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.94, per 1000 atoms: 0.62 Number of scatterers: 25726 At special positions: 0 Unit cell: (156, 142, 170, 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 123 16.00 O 4963 8.00 N 4206 7.00 C 16434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 351 " distance=2.10 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.05 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 514 " distance=2.08 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.02 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.04 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.04 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.12 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.02 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.22 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 351 " distance=2.10 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.05 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 514 " distance=2.08 Simple disulfide: pdb=" SG CYS B 469 " - pdb=" SG CYS B 477 " distance=2.02 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.04 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.04 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.12 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.02 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.22 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 351 " distance=2.10 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.05 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 514 " distance=2.08 Simple disulfide: pdb=" SG CYS C 469 " - pdb=" SG CYS C 477 " distance=2.02 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 579 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.04 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.04 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.12 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.02 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.22 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 ALPHA1-2 " MAN H 4 " - " MAN H 5 " " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA H 3 " - " MAN H 6 " " BMA R 3 " - " MAN R 6 " " BMA b 3 " - " MAN b 6 " BETA1-4 " 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 G 2 " - " BMA G 3 " " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " 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-ASN " NAG A1301 " - " ASN A 24 " " NAG A1302 " - " ASN A 159 " " NAG A1303 " - " ASN A 272 " " NAG A1304 " - " ASN A 333 " " NAG A1305 " - " ASN A 360 " " NAG A1306 " - " ASN A 592 " " NAG A1307 " - " ASN A 605 " " NAG A1308 " - " ASN A 648 " " NAG A1309 " - " ASN A1117 " " NAG A1310 " - " ASN A 148 " " NAG A1311 " - " ASN A1057 " " NAG B1301 " - " ASN B 24 " " NAG B1302 " - " ASN B 159 " " NAG B1303 " - " ASN B 272 " " NAG B1304 " - " ASN B 333 " " NAG B1305 " - " ASN B 360 " " NAG B1306 " - " ASN B 592 " " NAG B1307 " - " ASN B 605 " " NAG B1308 " - " ASN B 648 " " NAG B1309 " - " ASN B1117 " " NAG B1310 " - " ASN B 148 " " NAG B1311 " - " ASN B1057 " " NAG C1301 " - " ASN C 24 " " NAG C1302 " - " ASN C 159 " " NAG C1303 " - " ASN C 272 " " NAG C1304 " - " ASN C 333 " " NAG C1305 " - " ASN C 360 " " NAG C1306 " - " ASN C 592 " " NAG C1307 " - " ASN C 605 " " NAG C1308 " - " ASN C 648 " " NAG C1309 " - " ASN C1117 " " NAG C1310 " - " ASN C 148 " " NAG C1311 " - " ASN C1057 " " NAG D 1 " - " ASN A 65 " " NAG E 1 " - " ASN A 115 " " NAG F 1 " - " ASN A 125 " " NAG G 1 " - " ASN A 162 " " NAG H 1 " - " ASN A 230 " " NAG I 1 " - " ASN A 321 " " NAG J 1 " - " ASN A 692 " " NAG K 1 " - " ASN A 700 " " NAG L 1 " - " ASN A 784 " " NAG M 1 " - " ASN A1081 " " NAG N 1 " - " ASN B 65 " " NAG O 1 " - " ASN B 115 " " NAG P 1 " - " ASN B 125 " " NAG Q 1 " - " ASN B 162 " " NAG R 1 " - " ASN B 230 " " NAG S 1 " - " ASN B 321 " " NAG T 1 " - " ASN B 692 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN B 784 " " NAG W 1 " - " ASN B1081 " " NAG X 1 " - " ASN C 65 " " NAG Y 1 " - " ASN C 115 " " NAG Z 1 " - " ASN C 125 " " NAG a 1 " - " ASN C 162 " " NAG b 1 " - " ASN C 230 " " NAG c 1 " - " ASN C 321 " " NAG d 1 " - " ASN C 692 " " NAG e 1 " - " ASN C 700 " " NAG f 1 " - " ASN C 784 " " NAG g 1 " - " ASN C1081 " Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 3.1 seconds 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 54 sheets defined 24.9% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.375A pdb=" N SER A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 284 through 285 No H-bonds generated for 'chain 'A' and resid 284 through 285' Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.871A pdb=" N TRP A 343 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.280A pdb=" N ARG A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.723A pdb=" N SER A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.595A pdb=" N ILE A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 741 through 766 removed outlier: 3.803A pdb=" N ASP A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 849 through 866 removed outlier: 3.552A pdb=" N THR A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 902 through 923 removed outlier: 3.681A pdb=" N ILE A 917 " --> pdb=" O ALA A 913 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 918 " --> pdb=" O ILE A 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 928 through 947 removed outlier: 3.536A pdb=" N VAL A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 968 through 1015 removed outlier: 5.209A pdb=" N VAL A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 removed outlier: 4.375A pdb=" N SER B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 284 through 285 No H-bonds generated for 'chain 'B' and resid 284 through 285' Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.871A pdb=" N TRP B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.280A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.723A pdb=" N SER B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 622 through 627 Processing helix chain 'B' and resid 720 through 726 removed outlier: 3.594A pdb=" N ILE B 725 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 737 Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 741 through 766 removed outlier: 3.803A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 764 " --> pdb=" O ASN B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 832 through 839 Processing helix chain 'B' and resid 849 through 866 removed outlier: 3.552A pdb=" N THR B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 896 through 902 Processing helix chain 'B' and resid 902 through 923 removed outlier: 3.680A pdb=" N ILE B 917 " --> pdb=" O ALA B 913 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN B 918 " --> pdb=" O ILE B 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 919 " --> pdb=" O SER B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 927 Processing helix chain 'B' and resid 928 through 947 removed outlier: 3.536A pdb=" N VAL B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 959 through 967 Processing helix chain 'B' and resid 968 through 1015 removed outlier: 5.209A pdb=" N VAL B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 246 removed outlier: 4.375A pdb=" N SER C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.872A pdb=" N TRP C 343 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 396 through 401 removed outlier: 4.280A pdb=" N ARG C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.723A pdb=" N SER C 434 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 613 Processing helix chain 'C' and resid 622 through 627 Processing helix chain 'C' and resid 720 through 726 removed outlier: 3.594A pdb=" N ILE C 725 " --> pdb=" O CYS C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 741 through 766 removed outlier: 3.803A pdb=" N ASP C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 764 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 832 through 839 Processing helix chain 'C' and resid 849 through 866 removed outlier: 3.552A pdb=" N THR C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 896 through 902 Processing helix chain 'C' and resid 902 through 923 removed outlier: 3.681A pdb=" N ILE C 917 " --> pdb=" O ALA C 913 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 918 " --> pdb=" O ILE C 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP C 919 " --> pdb=" O SER C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 928 through 947 removed outlier: 3.536A pdb=" N VAL C 934 " --> pdb=" O LYS C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 959 through 967 Processing helix chain 'C' and resid 968 through 1015 removed outlier: 5.209A pdb=" N VAL C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.772A pdb=" N ASN A 65 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS A 259 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 184 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 183 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU A 197 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 224 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 199 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR A 203 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL A 218 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N ARG A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N PHE A 216 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ARG A 38 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU A 219 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE A 40 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 removed outlier: 4.069A pdb=" N ASP A 277 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 13.853A pdb=" N PHE A 234 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 13.711A pdb=" N PHE A 138 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N VAL A 236 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N GLN A 140 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N MET A 238 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 240 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 144 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR A 137 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 156 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N ASP A 141 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER A 154 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N MET A 143 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N TYR A 152 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR A 145 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER A 150 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.452A pdb=" N THR A 239 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 104 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG A 105 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 165 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 318 removed outlier: 5.098A pdb=" N ASP A 563 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 564 " --> pdb=" O GLY A 555 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 348 removed outlier: 4.014A pdb=" N VAL A 386 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 385 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 352 removed outlier: 6.462A pdb=" N CYS A 351 " --> pdb=" O CYS A 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 645 through 651 removed outlier: 6.250A pdb=" N THR A 645 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR A 679 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU A 647 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 685 through 686 Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A1059 " --> pdb=" O MET A1080 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A1061 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE A1078 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.252A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 771 through 772 removed outlier: 5.749A pdb=" N ILE A 771 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 867 through 868 Processing sheet with id=AC1, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AC2, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.772A pdb=" N ASN B 65 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B 259 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS B 184 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 183 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 197 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS B 224 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 199 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR B 203 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL B 218 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N ARG B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N PHE B 216 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG B 38 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU B 219 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE B 40 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 32 through 34 Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 59 removed outlier: 4.069A pdb=" N ASP B 277 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 88 removed outlier: 13.853A pdb=" N PHE B 234 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 13.711A pdb=" N PHE B 138 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N VAL B 236 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N GLN B 140 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N MET B 238 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 240 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 144 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR B 137 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 156 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N ASP B 141 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER B 154 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N MET B 143 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N TYR B 152 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR B 145 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER B 150 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.453A pdb=" N THR B 239 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 104 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG B 105 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 165 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 301 through 304 Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 318 removed outlier: 5.098A pdb=" N ASP B 563 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 564 " --> pdb=" O GLY B 555 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 344 through 348 removed outlier: 4.013A pdb=" N VAL B 386 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 385 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 351 through 352 removed outlier: 6.462A pdb=" N CYS B 351 " --> pdb=" O CYS B 514 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 441 through 443 Processing sheet with id=AD3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AD4, first strand: chain 'B' and resid 645 through 651 removed outlier: 6.250A pdb=" N THR B 645 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR B 679 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU B 647 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 685 through 686 Processing sheet with id=AD6, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B1059 " --> pdb=" O MET B1080 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B1061 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B1078 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.252A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 867 through 868 Processing sheet with id=AE1, first strand: chain 'B' and resid 1103 through 1105 Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.772A pdb=" N ASN C 65 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS C 259 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS C 184 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 183 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU C 197 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS C 224 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 199 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR C 203 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL C 218 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N ARG C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N PHE C 216 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG C 38 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU C 219 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE C 40 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AE4, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.068A pdb=" N ASP C 277 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 87 through 88 removed outlier: 13.853A pdb=" N PHE C 234 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 13.711A pdb=" N PHE C 138 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N VAL C 236 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N GLN C 140 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N MET C 238 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 240 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 144 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR C 137 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL C 156 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N ASP C 141 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER C 154 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N MET C 143 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N TYR C 152 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR C 145 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER C 150 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.453A pdb=" N THR C 239 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 104 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG C 105 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 165 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 318 removed outlier: 5.098A pdb=" N ASP C 563 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 564 " --> pdb=" O GLY C 555 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 344 through 348 removed outlier: 4.014A pdb=" N VAL C 386 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 385 " --> pdb=" O GLU C 505 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 351 through 352 removed outlier: 6.463A pdb=" N CYS C 351 " --> pdb=" O CYS C 514 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 441 through 443 Processing sheet with id=AF3, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AF4, first strand: chain 'C' and resid 645 through 651 removed outlier: 6.250A pdb=" N THR C 645 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR C 679 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU C 647 " --> pdb=" O THR C 679 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.288A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C1059 " --> pdb=" O MET C1080 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.252A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 867 through 868 Processing sheet with id=AF9, first strand: chain 'C' and resid 1103 through 1105 1058 hydrogen bonds defined for protein. 2904 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: 14.35 Time building geometry restraints manager: 7.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.50: 15841 1.50 - 1.84: 10464 1.84 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.87: 3 Bond restraints: 26308 Sorted by residual: bond pdb=" C PRO A 285 " pdb=" N LEU A 286 " ideal model delta sigma weight residual 1.335 2.866 -1.531 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C PRO B 285 " pdb=" N LEU B 286 " ideal model delta sigma weight residual 1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C PRO C 285 " pdb=" N LEU C 286 " ideal model delta sigma weight residual 1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C ASN A 148 " pdb=" O ASN A 148 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.29e-02 6.01e+03 3.29e+01 bond pdb=" C ASN C 148 " pdb=" O ASN C 148 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.29e-02 6.01e+03 3.27e+01 ... (remaining 26303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.59: 35782 6.59 - 13.17: 120 13.17 - 19.76: 3 19.76 - 26.34: 3 26.34 - 32.93: 3 Bond angle restraints: 35911 Sorted by residual: angle pdb=" C PRO B 285 " pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta sigma weight residual 120.72 87.79 32.93 1.67e+00 3.59e-01 3.89e+02 angle pdb=" C PRO A 285 " pdb=" N LEU A 286 " pdb=" CA LEU A 286 " ideal model delta sigma weight residual 120.72 87.80 32.92 1.67e+00 3.59e-01 3.89e+02 angle pdb=" C PRO C 285 " pdb=" N LEU C 286 " pdb=" CA LEU C 286 " ideal model delta sigma weight residual 120.72 87.82 32.90 1.67e+00 3.59e-01 3.88e+02 angle pdb=" N HIS C 614 " pdb=" CA HIS C 614 " pdb=" CB HIS C 614 " ideal model delta sigma weight residual 110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02 angle pdb=" N HIS B 614 " pdb=" CA HIS B 614 " pdb=" CB HIS B 614 " ideal model delta sigma weight residual 110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02 ... (remaining 35906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 16286 21.62 - 43.25: 488 43.25 - 64.87: 105 64.87 - 86.49: 54 86.49 - 108.12: 30 Dihedral angle restraints: 16963 sinusoidal: 7501 harmonic: 9462 Sorted by residual: dihedral pdb=" C LEU A 613 " pdb=" N LEU A 613 " pdb=" CA LEU A 613 " pdb=" CB LEU A 613 " ideal model delta harmonic sigma weight residual -122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02 dihedral pdb=" C LEU C 613 " pdb=" N LEU C 613 " pdb=" CA LEU C 613 " pdb=" CB LEU C 613 " ideal model delta harmonic sigma weight residual -122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02 dihedral pdb=" C LEU B 613 " pdb=" N LEU B 613 " pdb=" CA LEU B 613 " pdb=" CB LEU B 613 " ideal model delta harmonic sigma weight residual -122.60 -161.92 39.32 0 2.50e+00 1.60e-01 2.47e+02 ... (remaining 16960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4391 0.340 - 0.680: 18 0.680 - 1.020: 0 1.020 - 1.360: 0 1.360 - 1.700: 9 Chirality restraints: 4418 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 148 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 ... (remaining 4415 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO B 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO B 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU B 286 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO A 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO A 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU A 286 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO C 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO C 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU C 286 " -0.032 2.00e-02 2.50e+03 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 12786 2.97 - 3.46: 22373 3.46 - 3.94: 42075 3.94 - 4.42: 47191 4.42 - 4.90: 77853 Nonbonded interactions: 202278 Sorted by model distance: nonbonded pdb=" O GLY B 891 " pdb=" NZ LYS B1021 " model vdw 2.492 3.120 nonbonded pdb=" O GLY C 891 " pdb=" NZ LYS C1021 " model vdw 2.492 3.120 nonbonded pdb=" O GLY A 891 " pdb=" NZ LYS A1021 " model vdw 2.492 3.120 nonbonded pdb=" OD1 ASP C 44 " pdb=" N ASP C 45 " model vdw 2.528 3.120 nonbonded pdb=" OD1 ASP A 44 " pdb=" N ASP A 45 " model vdw 2.528 3.120 ... (remaining 202273 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' selection = (chain 'B' and (resid 18 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 1125 or resid 1301 thr \ ough 1311)) selection = (chain 'C' and (resid 18 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 559 or (resid 560 and \ (name N or name CA or name C or name O or name CB )) or resid 561 through 1125 o \ r resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'R' selection = chain 'b' } 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: 8.140 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: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 62.480 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.190 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.531 26461 Z= 1.370 Angle : 1.448 32.925 36328 Z= 0.926 Chirality : 0.117 1.700 4418 Planarity : 0.006 0.103 4525 Dihedral : 12.485 108.116 10765 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.44 % Rotamer: Outliers : 1.13 % Allowed : 1.38 % Favored : 97.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3222 helix: -0.11 (0.18), residues: 729 sheet: 1.20 (0.18), residues: 702 loop : -0.36 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP B1085 HIS 0.005 0.001 HIS B 128 PHE 0.021 0.003 PHE A 234 TYR 0.035 0.004 TYR B 203 ARG 0.005 0.000 ARG C 347 Details of bonding type rmsd link_NAG-ASN : bond 0.05346 ( 63) link_NAG-ASN : angle 3.30307 ( 189) link_ALPHA1-6 : bond 0.04586 ( 3) link_ALPHA1-6 : angle 1.61410 ( 9) link_BETA1-4 : bond 0.05770 ( 36) link_BETA1-4 : angle 2.86244 ( 108) link_ALPHA1-2 : bond 0.06459 ( 3) link_ALPHA1-2 : angle 2.63285 ( 9) link_ALPHA1-3 : bond 0.06156 ( 6) link_ALPHA1-3 : angle 2.17215 ( 18) hydrogen bonds : bond 0.20295 ( 1010) hydrogen bonds : angle 7.67629 ( 2904) SS BOND : bond 0.05932 ( 42) SS BOND : angle 4.31341 ( 84) covalent geometry : bond 0.02007 (26308) covalent geometry : angle 1.41067 (35911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6444 Ramachandran restraints generated. 3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 385 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1084 HIS cc_start: 0.7971 (m90) cc_final: 0.7724 (m90) REVERT: A 1102 ASN cc_start: 0.6093 (m-40) cc_final: 0.5721 (m-40) REVERT: B 166 ASN cc_start: 0.7638 (t0) cc_final: 0.7336 (t0) REVERT: B 952 ASN cc_start: 0.7475 (m-40) cc_final: 0.7226 (m-40) REVERT: B 976 ILE cc_start: 0.8452 (mt) cc_final: 0.8236 (mp) outliers start: 27 outliers final: 6 residues processed: 405 average time/residue: 1.3866 time to fit residues: 646.5480 Evaluate side-chains 198 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 905 GLN Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.8980 chunk 245 optimal weight: 0.6980 chunk 136 optimal weight: 0.0980 chunk 83 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 253 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 154 optimal weight: 0.4980 chunk 189 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 304 GLN A 474 GLN A 602 GLN A 738 GLN A 878 GLN A 988 GLN B 436 GLN B 602 GLN B 787 GLN B 918 GLN C 602 GLN C 787 GLN C 878 GLN C 918 GLN C 988 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125420 restraints weight = 29502.433| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.20 r_work: 0.3285 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26461 Z= 0.155 Angle : 0.695 30.171 36328 Z= 0.345 Chirality : 0.051 0.968 4418 Planarity : 0.004 0.035 4525 Dihedral : 9.929 93.867 5800 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.88 % Allowed : 8.39 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3228 helix: 1.42 (0.20), residues: 735 sheet: 1.43 (0.20), residues: 633 loop : -0.33 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 622 HIS 0.010 0.001 HIS A 184 PHE 0.016 0.001 PHE C 123 TYR 0.020 0.001 TYR B1050 ARG 0.006 0.001 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 63) link_NAG-ASN : angle 4.03553 ( 189) link_ALPHA1-6 : bond 0.01286 ( 3) link_ALPHA1-6 : angle 1.40678 ( 9) link_BETA1-4 : bond 0.00709 ( 36) link_BETA1-4 : angle 1.91488 ( 108) link_ALPHA1-2 : bond 0.00396 ( 3) link_ALPHA1-2 : angle 2.05913 ( 9) link_ALPHA1-3 : bond 0.01774 ( 6) link_ALPHA1-3 : angle 1.48696 ( 18) hydrogen bonds : bond 0.07016 ( 1010) hydrogen bonds : angle 5.79883 ( 2904) SS BOND : bond 0.00333 ( 42) SS BOND : angle 1.50776 ( 84) covalent geometry : bond 0.00316 (26308) covalent geometry : angle 0.61994 (35911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7986 (mm110) REVERT: A 762 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7607 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8499 (m90) cc_final: 0.8210 (m90) REVERT: B 184 HIS cc_start: 0.6747 (m-70) cc_final: 0.5290 (p90) REVERT: B 344 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 806 TYR cc_start: 0.7440 (m-80) cc_final: 0.7131 (m-80) REVERT: B 952 ASN cc_start: 0.8324 (m-40) cc_final: 0.8093 (m-40) REVERT: B 1033 MET cc_start: 0.8931 (ptm) cc_final: 0.8570 (ptp) REVERT: C 205 ARG cc_start: 0.7023 (ttm-80) cc_final: 0.6345 (mmm160) REVERT: C 723 MET cc_start: 0.9090 (ttt) cc_final: 0.8866 (ttm) REVERT: C 916 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6718 (mppt) outliers start: 45 outliers final: 11 residues processed: 259 average time/residue: 1.2694 time to fit residues: 387.0358 Evaluate side-chains 197 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 916 LYS Chi-restraints excluded: chain C residue 947 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 247 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 314 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 315 optimal weight: 0.9990 chunk 262 optimal weight: 0.0030 chunk 318 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 304 GLN A 324 ASN A 878 GLN B 201 HIS B 324 ASN B 436 GLN C 118 GLN C 201 HIS C 324 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123136 restraints weight = 29383.956| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.23 r_work: 0.3247 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26461 Z= 0.141 Angle : 0.675 26.806 36328 Z= 0.323 Chirality : 0.053 1.176 4418 Planarity : 0.004 0.034 4525 Dihedral : 8.543 88.957 5789 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.75 % Allowed : 9.01 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3228 helix: 1.41 (0.20), residues: 756 sheet: 1.25 (0.20), residues: 657 loop : -0.50 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 622 HIS 0.005 0.001 HIS B 151 PHE 0.018 0.002 PHE B1104 TYR 0.020 0.001 TYR B1050 ARG 0.006 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 63) link_NAG-ASN : angle 4.34629 ( 189) link_ALPHA1-6 : bond 0.01441 ( 3) link_ALPHA1-6 : angle 1.21405 ( 9) link_BETA1-4 : bond 0.00633 ( 36) link_BETA1-4 : angle 1.62879 ( 108) link_ALPHA1-2 : bond 0.00352 ( 3) link_ALPHA1-2 : angle 1.99741 ( 9) link_ALPHA1-3 : bond 0.01572 ( 6) link_ALPHA1-3 : angle 1.06089 ( 18) hydrogen bonds : bond 0.06056 ( 1010) hydrogen bonds : angle 5.35677 ( 2904) SS BOND : bond 0.00238 ( 42) SS BOND : angle 1.32137 ( 84) covalent geometry : bond 0.00298 (26308) covalent geometry : angle 0.58938 (35911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8203 (tt) cc_final: 0.7900 (tp) REVERT: A 233 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7987 (mm110) REVERT: A 517 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.6857 (mmtm) REVERT: A 547 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8227 (mptt) REVERT: A 714 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: A 762 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7620 (ttp-110) REVERT: A 1069 LYS cc_start: 0.7849 (mtmp) cc_final: 0.7604 (mtpt) REVERT: A 1084 HIS cc_start: 0.8505 (m90) cc_final: 0.8218 (m90) REVERT: B 184 HIS cc_start: 0.6463 (m-70) cc_final: 0.5198 (p90) REVERT: B 748 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7504 (mtm-85) REVERT: B 759 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.6852 (ttm-80) REVERT: C 205 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.6500 (mmm160) REVERT: C 723 MET cc_start: 0.9089 (ttt) cc_final: 0.8827 (ttm) REVERT: C 759 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.6931 (ttm-80) outliers start: 42 outliers final: 10 residues processed: 235 average time/residue: 1.2948 time to fit residues: 358.3280 Evaluate side-chains 198 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 883 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 279 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 0.0470 chunk 162 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 231 optimal weight: 0.1980 chunk 283 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS A 304 GLN A 324 ASN A 602 GLN B 151 HIS B 324 ASN C 324 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120572 restraints weight = 29740.955| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.29 r_work: 0.3206 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26461 Z= 0.170 Angle : 0.682 25.875 36328 Z= 0.326 Chirality : 0.051 0.680 4418 Planarity : 0.004 0.036 4525 Dihedral : 7.983 86.512 5787 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.59 % Allowed : 9.89 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3228 helix: 1.48 (0.20), residues: 732 sheet: 1.13 (0.19), residues: 708 loop : -0.64 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 427 HIS 0.010 0.002 HIS C 151 PHE 0.016 0.002 PHE B 665 TYR 0.022 0.002 TYR C 484 ARG 0.007 0.001 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 63) link_NAG-ASN : angle 4.26063 ( 189) link_ALPHA1-6 : bond 0.01449 ( 3) link_ALPHA1-6 : angle 1.26267 ( 9) link_BETA1-4 : bond 0.00553 ( 36) link_BETA1-4 : angle 1.57352 ( 108) link_ALPHA1-2 : bond 0.00182 ( 3) link_ALPHA1-2 : angle 1.86581 ( 9) link_ALPHA1-3 : bond 0.01440 ( 6) link_ALPHA1-3 : angle 1.24522 ( 18) hydrogen bonds : bond 0.06210 ( 1010) hydrogen bonds : angle 5.32722 ( 2904) SS BOND : bond 0.00253 ( 42) SS BOND : angle 1.16928 ( 84) covalent geometry : bond 0.00394 (26308) covalent geometry : angle 0.60160 (35911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8276 (tt) cc_final: 0.8012 (tp) REVERT: A 233 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7955 (mm110) REVERT: A 517 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.6875 (mmtm) REVERT: A 547 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8341 (mptt) REVERT: A 714 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8328 (mtm) REVERT: A 762 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7683 (ttp-110) REVERT: A 1069 LYS cc_start: 0.7901 (mtmp) cc_final: 0.7694 (mtpt) REVERT: A 1084 HIS cc_start: 0.8526 (m90) cc_final: 0.8224 (m90) REVERT: A 1102 ASN cc_start: 0.7000 (m-40) cc_final: 0.6572 (m110) REVERT: B 205 ARG cc_start: 0.7196 (ttm-80) cc_final: 0.6666 (mmm160) REVERT: B 627 LEU cc_start: 0.7463 (mt) cc_final: 0.7262 (mm) REVERT: B 937 GLN cc_start: 0.8294 (mt0) cc_final: 0.7577 (pt0) REVERT: C 205 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.6471 (mmm160) REVERT: C 759 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7060 (ttm-80) REVERT: C 1102 ASN cc_start: 0.7264 (m-40) cc_final: 0.6742 (m110) outliers start: 38 outliers final: 14 residues processed: 229 average time/residue: 1.1908 time to fit residues: 322.9443 Evaluate side-chains 211 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 883 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 28 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 263 optimal weight: 0.0770 chunk 119 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 166 optimal weight: 0.2980 chunk 165 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 279 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN C 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123710 restraints weight = 29246.958| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.21 r_work: 0.3229 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26461 Z= 0.117 Angle : 0.608 23.294 36328 Z= 0.291 Chirality : 0.049 0.544 4418 Planarity : 0.004 0.038 4525 Dihedral : 7.344 82.540 5787 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.67 % Allowed : 10.14 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3228 helix: 1.75 (0.20), residues: 732 sheet: 1.11 (0.19), residues: 708 loop : -0.63 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 622 HIS 0.004 0.001 HIS C 151 PHE 0.014 0.001 PHE C 123 TYR 0.019 0.001 TYR B1050 ARG 0.006 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 63) link_NAG-ASN : angle 4.04693 ( 189) link_ALPHA1-6 : bond 0.01544 ( 3) link_ALPHA1-6 : angle 1.12324 ( 9) link_BETA1-4 : bond 0.00528 ( 36) link_BETA1-4 : angle 1.51814 ( 108) link_ALPHA1-2 : bond 0.00225 ( 3) link_ALPHA1-2 : angle 1.76750 ( 9) link_ALPHA1-3 : bond 0.01493 ( 6) link_ALPHA1-3 : angle 1.19596 ( 18) hydrogen bonds : bond 0.05266 ( 1010) hydrogen bonds : angle 5.10016 ( 2904) SS BOND : bond 0.00199 ( 42) SS BOND : angle 0.80369 ( 84) covalent geometry : bond 0.00237 (26308) covalent geometry : angle 0.52721 (35911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8231 (tt) cc_final: 0.8012 (tp) REVERT: A 233 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7914 (mm110) REVERT: A 547 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8349 (mptt) REVERT: A 714 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8392 (mtp) REVERT: A 759 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.6963 (ttm-80) REVERT: A 762 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7694 (ttp-110) REVERT: A 993 GLN cc_start: 0.8254 (mt0) cc_final: 0.8045 (mm-40) REVERT: A 1084 HIS cc_start: 0.8555 (m90) cc_final: 0.8262 (m90) REVERT: B 205 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6671 (mmm160) REVERT: B 595 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7596 (mmtt) REVERT: B 759 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.6774 (ttm-80) REVERT: B 937 GLN cc_start: 0.8304 (mt0) cc_final: 0.7608 (pt0) REVERT: C 184 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6421 (m90) REVERT: C 759 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.7031 (ttm-80) REVERT: C 993 GLN cc_start: 0.8452 (mt0) cc_final: 0.8123 (mm-40) REVERT: C 1102 ASN cc_start: 0.7096 (m-40) cc_final: 0.6513 (m110) outliers start: 40 outliers final: 21 residues processed: 237 average time/residue: 1.2432 time to fit residues: 347.3271 Evaluate side-chains 217 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 30 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 167 optimal weight: 0.4980 chunk 246 optimal weight: 3.9990 chunk 283 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 304 GLN A 324 ASN B 135 ASN B 324 ASN C 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118947 restraints weight = 29228.606| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.23 r_work: 0.3155 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26461 Z= 0.204 Angle : 0.693 21.891 36328 Z= 0.336 Chirality : 0.052 0.504 4418 Planarity : 0.005 0.041 4525 Dihedral : 7.661 83.604 5787 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.50 % Allowed : 9.51 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3228 helix: 1.43 (0.19), residues: 735 sheet: 1.07 (0.19), residues: 723 loop : -0.89 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 427 HIS 0.008 0.002 HIS C 201 PHE 0.017 0.002 PHE A 665 TYR 0.026 0.002 TYR C 484 ARG 0.007 0.001 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 63) link_NAG-ASN : angle 4.04576 ( 189) link_ALPHA1-6 : bond 0.01364 ( 3) link_ALPHA1-6 : angle 1.25913 ( 9) link_BETA1-4 : bond 0.00519 ( 36) link_BETA1-4 : angle 1.58983 ( 108) link_ALPHA1-2 : bond 0.00124 ( 3) link_ALPHA1-2 : angle 1.81424 ( 9) link_ALPHA1-3 : bond 0.01269 ( 6) link_ALPHA1-3 : angle 1.34663 ( 18) hydrogen bonds : bond 0.06537 ( 1010) hydrogen bonds : angle 5.35182 ( 2904) SS BOND : bond 0.00272 ( 42) SS BOND : angle 1.20140 ( 84) covalent geometry : bond 0.00490 (26308) covalent geometry : angle 0.62159 (35911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 2.632 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8450 (tt) cc_final: 0.8221 (tp) REVERT: A 233 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8116 (mm110) REVERT: A 344 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: A 714 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8441 (mtm) REVERT: A 762 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7940 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8604 (m90) cc_final: 0.8305 (m90) REVERT: A 1102 ASN cc_start: 0.7668 (m-40) cc_final: 0.7459 (m-40) REVERT: B 205 ARG cc_start: 0.7341 (ttm-80) cc_final: 0.6778 (mmm160) REVERT: B 738 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8224 (mm-40) REVERT: B 937 GLN cc_start: 0.8483 (mt0) cc_final: 0.7846 (pt0) REVERT: C 122 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8032 (tp) REVERT: C 184 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6592 (m90) REVERT: C 347 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7852 (ttt-90) REVERT: C 759 ARG cc_start: 0.7904 (ttp-170) cc_final: 0.7409 (ttm-80) REVERT: C 993 GLN cc_start: 0.8565 (mt0) cc_final: 0.8290 (mm-40) outliers start: 60 outliers final: 27 residues processed: 237 average time/residue: 1.2356 time to fit residues: 344.9577 Evaluate side-chains 227 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 34 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 311 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 324 ASN B 135 ASN B 324 ASN C 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118454 restraints weight = 29624.130| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.25 r_work: 0.3156 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26461 Z= 0.196 Angle : 0.686 21.040 36328 Z= 0.331 Chirality : 0.051 0.492 4418 Planarity : 0.005 0.042 4525 Dihedral : 7.828 82.884 5787 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.50 % Allowed : 9.85 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3228 helix: 1.43 (0.19), residues: 735 sheet: 1.04 (0.19), residues: 747 loop : -1.05 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 622 HIS 0.007 0.002 HIS C 201 PHE 0.022 0.002 PHE B 665 TYR 0.023 0.002 TYR C 484 ARG 0.007 0.001 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 63) link_NAG-ASN : angle 4.20051 ( 189) link_ALPHA1-6 : bond 0.01387 ( 3) link_ALPHA1-6 : angle 1.11706 ( 9) link_BETA1-4 : bond 0.00494 ( 36) link_BETA1-4 : angle 1.61705 ( 108) link_ALPHA1-2 : bond 0.00126 ( 3) link_ALPHA1-2 : angle 1.84438 ( 9) link_ALPHA1-3 : bond 0.01290 ( 6) link_ALPHA1-3 : angle 1.29276 ( 18) hydrogen bonds : bond 0.06379 ( 1010) hydrogen bonds : angle 5.30113 ( 2904) SS BOND : bond 0.00271 ( 42) SS BOND : angle 1.22161 ( 84) covalent geometry : bond 0.00469 (26308) covalent geometry : angle 0.60803 (35911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8082 (mm110) REVERT: A 344 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: A 762 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7960 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8611 (m90) cc_final: 0.8293 (m90) REVERT: B 165 TYR cc_start: 0.7468 (t80) cc_final: 0.7234 (t80) REVERT: B 205 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6729 (mmm160) REVERT: B 937 GLN cc_start: 0.8454 (mt0) cc_final: 0.7865 (pt0) REVERT: B 1102 ASN cc_start: 0.8194 (m-40) cc_final: 0.7993 (m110) REVERT: C 122 LEU cc_start: 0.8364 (tt) cc_final: 0.8131 (tp) REVERT: C 184 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.6510 (m90) REVERT: C 233 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: C 347 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7835 (ttt-90) REVERT: C 759 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7417 (ttm-80) outliers start: 60 outliers final: 29 residues processed: 239 average time/residue: 1.1680 time to fit residues: 330.6229 Evaluate side-chains 226 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 981 THR Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 242 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 241 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 282 optimal weight: 0.0060 chunk 178 optimal weight: 1.9990 chunk 259 optimal weight: 0.0670 chunk 97 optimal weight: 0.4980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A1054 GLN B 324 ASN B 738 GLN B 988 GLN C 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.152771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121488 restraints weight = 29420.453| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.22 r_work: 0.3212 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26461 Z= 0.111 Angle : 0.608 20.552 36328 Z= 0.291 Chirality : 0.047 0.436 4418 Planarity : 0.004 0.041 4525 Dihedral : 7.376 79.178 5787 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.29 % Allowed : 11.35 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3228 helix: 1.83 (0.20), residues: 738 sheet: 0.98 (0.19), residues: 738 loop : -0.92 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 622 HIS 0.002 0.001 HIS A 201 PHE 0.026 0.001 PHE B 665 TYR 0.020 0.001 TYR B1050 ARG 0.007 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 63) link_NAG-ASN : angle 3.91770 ( 189) link_ALPHA1-6 : bond 0.01540 ( 3) link_ALPHA1-6 : angle 1.01016 ( 9) link_BETA1-4 : bond 0.00485 ( 36) link_BETA1-4 : angle 1.54395 ( 108) link_ALPHA1-2 : bond 0.00190 ( 3) link_ALPHA1-2 : angle 1.75762 ( 9) link_ALPHA1-3 : bond 0.01402 ( 6) link_ALPHA1-3 : angle 1.14483 ( 18) hydrogen bonds : bond 0.05171 ( 1010) hydrogen bonds : angle 5.02145 ( 2904) SS BOND : bond 0.00187 ( 42) SS BOND : angle 0.88305 ( 84) covalent geometry : bond 0.00223 (26308) covalent geometry : angle 0.53162 (35911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8040 (mm110) REVERT: A 344 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: A 759 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7399 (ttm-80) REVERT: A 762 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7860 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8575 (m90) cc_final: 0.8269 (m90) REVERT: A 1102 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7206 (m110) REVERT: B 165 TYR cc_start: 0.7458 (t80) cc_final: 0.7220 (t80) REVERT: B 205 ARG cc_start: 0.7252 (ttm-80) cc_final: 0.6691 (mmm160) REVERT: B 304 GLN cc_start: 0.8117 (mp10) cc_final: 0.7670 (mm-40) REVERT: B 937 GLN cc_start: 0.8455 (mt0) cc_final: 0.7852 (pt0) REVERT: C 122 LEU cc_start: 0.8277 (tt) cc_final: 0.8062 (tp) REVERT: C 184 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6504 (m90) REVERT: C 759 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7348 (ttm-80) REVERT: C 993 GLN cc_start: 0.8558 (mt0) cc_final: 0.8279 (mm-40) outliers start: 31 outliers final: 18 residues processed: 221 average time/residue: 1.3023 time to fit residues: 340.2745 Evaluate side-chains 213 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 947 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 222 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 304 GLN A 324 ASN A 918 GLN B 324 ASN C 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115884 restraints weight = 29737.930| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.34 r_work: 0.3120 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26461 Z= 0.224 Angle : 0.713 20.207 36328 Z= 0.344 Chirality : 0.053 0.637 4418 Planarity : 0.005 0.045 4525 Dihedral : 7.849 81.520 5787 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.63 % Allowed : 11.31 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3228 helix: 1.32 (0.19), residues: 756 sheet: 1.03 (0.19), residues: 741 loop : -1.18 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 427 HIS 0.009 0.002 HIS B 201 PHE 0.023 0.002 PHE B 665 TYR 0.026 0.002 TYR C 484 ARG 0.007 0.001 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 63) link_NAG-ASN : angle 4.14019 ( 189) link_ALPHA1-6 : bond 0.01305 ( 3) link_ALPHA1-6 : angle 1.18833 ( 9) link_BETA1-4 : bond 0.00496 ( 36) link_BETA1-4 : angle 1.57716 ( 108) link_ALPHA1-2 : bond 0.00079 ( 3) link_ALPHA1-2 : angle 1.78914 ( 9) link_ALPHA1-3 : bond 0.01165 ( 6) link_ALPHA1-3 : angle 1.36679 ( 18) hydrogen bonds : bond 0.06600 ( 1010) hydrogen bonds : angle 5.28905 ( 2904) SS BOND : bond 0.00293 ( 42) SS BOND : angle 1.39599 ( 84) covalent geometry : bond 0.00548 (26308) covalent geometry : angle 0.63990 (35911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8070 (mm-40) REVERT: A 344 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: A 748 ARG cc_start: 0.7559 (ttp80) cc_final: 0.7353 (mtm-85) REVERT: A 762 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7659 (ttp-110) REVERT: A 947 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7890 (tppt) REVERT: A 1084 HIS cc_start: 0.8530 (m90) cc_final: 0.8206 (m90) REVERT: B 165 TYR cc_start: 0.7436 (t80) cc_final: 0.7226 (t80) REVERT: B 205 ARG cc_start: 0.7280 (ttm-80) cc_final: 0.6541 (mmm160) REVERT: B 937 GLN cc_start: 0.8352 (mt0) cc_final: 0.7593 (pt0) REVERT: B 1102 ASN cc_start: 0.8193 (m-40) cc_final: 0.7946 (m110) REVERT: C 122 LEU cc_start: 0.8312 (tt) cc_final: 0.8063 (tp) REVERT: C 205 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.6474 (mmm160) REVERT: C 347 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7690 (ttt-90) REVERT: C 759 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7082 (ttm-80) outliers start: 39 outliers final: 29 residues processed: 221 average time/residue: 1.1366 time to fit residues: 297.9898 Evaluate side-chains 219 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 292 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 137 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 320 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 136 optimal weight: 0.3980 chunk 296 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN B 734 ASN C 135 ASN C 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119454 restraints weight = 29615.593| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.39 r_work: 0.3176 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26461 Z= 0.118 Angle : 0.617 20.088 36328 Z= 0.296 Chirality : 0.048 0.586 4418 Planarity : 0.004 0.058 4525 Dihedral : 7.711 91.734 5787 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.34 % Allowed : 11.81 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3228 helix: 1.80 (0.20), residues: 738 sheet: 0.95 (0.19), residues: 735 loop : -0.99 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 622 HIS 0.003 0.001 HIS A 201 PHE 0.025 0.001 PHE C1104 TYR 0.020 0.001 TYR B1050 ARG 0.007 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 63) link_NAG-ASN : angle 3.94966 ( 189) link_ALPHA1-6 : bond 0.01562 ( 3) link_ALPHA1-6 : angle 0.99229 ( 9) link_BETA1-4 : bond 0.00485 ( 36) link_BETA1-4 : angle 1.55711 ( 108) link_ALPHA1-2 : bond 0.00195 ( 3) link_ALPHA1-2 : angle 1.72046 ( 9) link_ALPHA1-3 : bond 0.01359 ( 6) link_ALPHA1-3 : angle 1.14255 ( 18) hydrogen bonds : bond 0.05250 ( 1010) hydrogen bonds : angle 5.01173 ( 2904) SS BOND : bond 0.00201 ( 42) SS BOND : angle 0.86019 ( 84) covalent geometry : bond 0.00246 (26308) covalent geometry : angle 0.54017 (35911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7844 (mm110) REVERT: A 344 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: A 759 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7069 (ttm-80) REVERT: A 762 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7624 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8532 (m90) cc_final: 0.8221 (m90) REVERT: B 165 TYR cc_start: 0.7463 (t80) cc_final: 0.7242 (t80) REVERT: B 205 ARG cc_start: 0.7316 (ttm-80) cc_final: 0.6605 (mmm160) REVERT: B 937 GLN cc_start: 0.8305 (mt0) cc_final: 0.7581 (pt0) REVERT: C 122 LEU cc_start: 0.8205 (tt) cc_final: 0.7934 (tp) REVERT: C 184 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6370 (m90) REVERT: C 759 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7003 (ttm-80) outliers start: 32 outliers final: 20 residues processed: 216 average time/residue: 1.1780 time to fit residues: 301.7311 Evaluate side-chains 212 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 236 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 292 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A1102 ASN B 324 ASN C 324 ASN C 738 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118996 restraints weight = 29414.210| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.35 r_work: 0.3182 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26461 Z= 0.144 Angle : 0.635 19.818 36328 Z= 0.306 Chirality : 0.049 0.461 4418 Planarity : 0.004 0.053 4525 Dihedral : 7.444 86.882 5787 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.25 % Allowed : 11.89 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3228 helix: 1.60 (0.19), residues: 756 sheet: 0.92 (0.19), residues: 735 loop : -1.08 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 427 HIS 0.005 0.001 HIS B 201 PHE 0.021 0.002 PHE C1104 TYR 0.018 0.001 TYR B1050 ARG 0.007 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 63) link_NAG-ASN : angle 4.00596 ( 189) link_ALPHA1-6 : bond 0.01460 ( 3) link_ALPHA1-6 : angle 1.09734 ( 9) link_BETA1-4 : bond 0.00477 ( 36) link_BETA1-4 : angle 1.52547 ( 108) link_ALPHA1-2 : bond 0.00148 ( 3) link_ALPHA1-2 : angle 1.70123 ( 9) link_ALPHA1-3 : bond 0.01206 ( 6) link_ALPHA1-3 : angle 1.19454 ( 18) hydrogen bonds : bond 0.05591 ( 1010) hydrogen bonds : angle 5.05775 ( 2904) SS BOND : bond 0.00214 ( 42) SS BOND : angle 1.01665 ( 84) covalent geometry : bond 0.00329 (26308) covalent geometry : angle 0.55854 (35911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17499.56 seconds wall clock time: 302 minutes 9.78 seconds (18129.78 seconds total)