Starting phenix.real_space_refine on Sun Jul 5 05:47:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_41842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_41842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_41842.cif" model { file = "/net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_41842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_41842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_41842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u29_41842/07_2026/8u29_41842.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 3, 'GLU:plan': 11, 'ASP:plan': 16, 'ASN:plan1': 7, 'TYR:plan': 2, 'GLN:plan1': 4} 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: {'ARG:plan': 3, 'GLU:plan': 11, 'ASP:plan': 16, 'ASN:plan1': 7, 'TYR:plan': 2, 'GLN:plan1': 4} 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: {'ARG:plan': 3, 'GLU:plan': 11, 'ASP:plan': 15, 'ASN:plan1': 7, 'TYR:plan': 2, 'GLN:plan1': 4} 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6.40, per 1000 atoms: 0.25 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: 2.38 Conformation dependent library (CDL) restraints added in 985.0 milliseconds 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: 0.85 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: 6.45 Time building geometry restraints manager: 3.15 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 - 17.68: 15804 17.68 - 35.35: 610 35.35 - 53.03: 141 53.03 - 70.70: 51 70.70 - 88.38: 15 Dihedral angle restraints: 16621 sinusoidal: 7159 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 16618 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 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 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: 16.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.100 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 10.400 87.085 10423 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (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 ARG 0.005 0.000 ARG C 347 TYR 0.035 0.004 TYR B 203 PHE 0.021 0.003 PHE A 234 TRP 0.026 0.005 TRP B1085 HIS 0.005 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.02007 / 1.36 (26308) covalent geometry : angle 1.41067 / 0.92 (35911) SS BOND : bond 0.05932 / 4.03 ( 42) SS BOND : angle 4.31341 / 2.92 ( 84) hydrogen bonds : bond 0.20295 / 13.98 ( 1010) hydrogen bonds : angle 7.67629 / 5.41 ( 2904) link_ALPHA1-2 : bond 0.06459 / 3.63 ( 3) link_ALPHA1-2 : angle 2.63285 / 1.27 ( 9) link_ALPHA1-3 : bond 0.06156 / 4.11 ( 6) link_ALPHA1-3 : angle 2.17215 / 1.68 ( 18) link_ALPHA1-6 : bond 0.04586 / 2.58 ( 3) link_ALPHA1-6 : angle 1.61410 / 0.77 ( 9) link_BETA1-4 : bond 0.05770 / 3.87 ( 36) link_BETA1-4 : angle 2.86244 / 1.91 ( 108) link_NAG-ASN : bond 0.05346 / 3.53 ( 63) link_NAG-ASN : angle 3.30307 / 2.73 ( 189) *********************** 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 : 0.905 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: 0.7225 (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: 0.6446 time to fit residues: 300.6264 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 : 1.078 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 201 HIS A 304 GLN A 474 GLN A 602 GLN A 738 GLN A 878 GLN A 988 GLN B 201 HIS 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121663 restraints weight = 29665.019| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.25 r_work: 0.3231 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26461 Z= 0.188 Angle : 0.721 29.664 36328 Z= 0.360 Chirality : 0.052 1.058 4418 Planarity : 0.005 0.036 4525 Dihedral : 6.494 59.517 5458 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.21 % Allowed : 8.01 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3228 helix: 1.08 (0.20), residues: 753 sheet: 1.34 (0.19), residues: 669 loop : -0.52 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.025 0.002 TYR C 484 PHE 0.017 0.002 PHE C 123 TRP 0.013 0.002 TRP C 622 HIS 0.010 0.002 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (26308) covalent geometry : angle 0.64968 / 0.34 (35911) SS BOND : bond 0.00349 / 0.25 ( 42) SS BOND : angle 1.73373 / 1.02 ( 84) hydrogen bonds : bond 0.07186 / 5.02 ( 1010) hydrogen bonds : angle 5.78253 / 4.07 ( 2904) link_ALPHA1-2 : bond 0.00425 / 0.24 ( 3) link_ALPHA1-2 : angle 1.78922 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01244 / 0.83 ( 6) link_ALPHA1-3 : angle 1.23915 / 0.84 ( 18) link_ALPHA1-6 : bond 0.00952 / 0.54 ( 3) link_ALPHA1-6 : angle 1.26988 / 0.70 ( 9) link_BETA1-4 : bond 0.00744 / 0.50 ( 36) link_BETA1-4 : angle 1.86797 / 1.29 ( 108) link_NAG-ASN : bond 0.00623 / 0.46 ( 63) link_NAG-ASN : angle 4.01460 / 2.54 ( 189) *********************** 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 285 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8092 (tt) cc_final: 0.7700 (tp) REVERT: A 233 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8071 (mm110) REVERT: A 762 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7669 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8550 (m90) cc_final: 0.8240 (m90) REVERT: A 1102 ASN cc_start: 0.6881 (m-40) cc_final: 0.6608 (m-40) REVERT: B 184 HIS cc_start: 0.6716 (m-70) cc_final: 0.5193 (p90) REVERT: B 759 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7302 (mtm-85) REVERT: B 806 TYR cc_start: 0.7555 (m-80) cc_final: 0.7345 (m-80) REVERT: B 1002 ARG cc_start: 0.8642 (tpt170) cc_final: 0.8373 (tpt170) REVERT: C 205 ARG cc_start: 0.7139 (ttm-80) cc_final: 0.6348 (mmm160) REVERT: C 595 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.6902 (mttt) outliers start: 53 outliers final: 15 residues processed: 255 average time/residue: 0.6196 time to fit residues: 185.3790 Evaluate side-chains 209 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 615 VAL Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 286 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 320 optimal weight: 0.5980 chunk 229 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS A 304 GLN A 324 ASN B 324 ASN B 436 GLN B 952 ASN C 201 HIS C 324 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121546 restraints weight = 29443.612| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.25 r_work: 0.3193 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2394 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= 0.167 Angle : 0.689 25.872 36328 Z= 0.335 Chirality : 0.054 1.386 4418 Planarity : 0.004 0.035 4525 Dihedral : 5.870 58.584 5451 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.13 % Allowed : 8.76 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3228 helix: 1.33 (0.20), residues: 732 sheet: 1.03 (0.19), residues: 687 loop : -0.61 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.024 0.002 TYR C 484 PHE 0.014 0.002 PHE A 665 TRP 0.011 0.002 TRP B 427 HIS 0.006 0.002 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (26308) covalent geometry : angle 0.60869 / 0.32 (35911) SS BOND : bond 0.00291 / 0.20 ( 42) SS BOND : angle 1.43462 / 0.88 ( 84) hydrogen bonds : bond 0.06531 / 4.56 ( 1010) hydrogen bonds : angle 5.48675 / 3.86 ( 2904) link_ALPHA1-2 : bond 0.00306 / 0.17 ( 3) link_ALPHA1-2 : angle 1.61189 / 0.87 ( 9) link_ALPHA1-3 : bond 0.01121 / 0.75 ( 6) link_ALPHA1-3 : angle 1.26212 / 0.89 ( 18) link_ALPHA1-6 : bond 0.01343 / 0.75 ( 3) link_ALPHA1-6 : angle 1.29249 / 0.71 ( 9) link_BETA1-4 : bond 0.00570 / 0.38 ( 36) link_BETA1-4 : angle 1.60457 / 1.10 ( 108) link_NAG-ASN : bond 0.00537 / 0.39 ( 63) link_NAG-ASN : angle 4.27031 / 3.07 ( 189) *********************** 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 270 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8324 (tt) cc_final: 0.8043 (tp) REVERT: A 233 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8092 (mm110) REVERT: A 517 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.6921 (mmtm) REVERT: A 547 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8380 (mptt) REVERT: A 714 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8497 (mtp) REVERT: A 762 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7846 (ttp-110) REVERT: A 1069 LYS cc_start: 0.8014 (mtmp) cc_final: 0.7771 (mtpt) REVERT: A 1084 HIS cc_start: 0.8580 (m90) cc_final: 0.8273 (m90) REVERT: B 184 HIS cc_start: 0.6635 (m-70) cc_final: 0.5415 (p90) REVERT: B 937 GLN cc_start: 0.8434 (mt0) cc_final: 0.7785 (pt0) REVERT: B 1002 ARG cc_start: 0.8728 (tpt170) cc_final: 0.8520 (tpt170) REVERT: C 205 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.6605 (mmm160) REVERT: C 347 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7801 (ttt-90) REVERT: C 759 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7355 (ttm-80) REVERT: C 1102 ASN cc_start: 0.7351 (m-40) cc_final: 0.6845 (m110) outliers start: 51 outliers final: 20 residues processed: 241 average time/residue: 0.6277 time to fit residues: 177.4882 Evaluate side-chains 210 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 A residue 947 LYS Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL 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 B residue 947 LYS Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 347 ARG 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 Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 309 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 296 optimal weight: 0.0270 chunk 151 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 304 GLN A 324 ASN A 602 GLN A 918 GLN B 151 HIS B 324 ASN C 324 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.151235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122319 restraints weight = 29149.486| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.02 r_work: 0.3068 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 26461 Z= 0.231 Angle : 0.765 25.796 36328 Z= 0.367 Chirality : 0.056 1.123 4418 Planarity : 0.005 0.045 4525 Dihedral : 6.133 57.819 5451 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.75 % Allowed : 9.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3228 helix: 1.07 (0.19), residues: 735 sheet: 0.85 (0.19), residues: 753 loop : -0.87 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 455 TYR 0.029 0.002 TYR C 484 PHE 0.022 0.002 PHE B1104 TRP 0.015 0.002 TRP A 427 HIS 0.010 0.003 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 (26308) covalent geometry : angle 0.68123 / 0.35 (35911) SS BOND : bond 0.00306 / 0.22 ( 42) SS BOND : angle 1.41230 / 0.89 ( 84) hydrogen bonds : bond 0.07034 / 4.89 ( 1010) hydrogen bonds : angle 5.52175 / 3.88 ( 2904) link_ALPHA1-2 : bond 0.00101 / 0.06 ( 3) link_ALPHA1-2 : angle 1.63741 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00950 / 0.63 ( 6) link_ALPHA1-3 : angle 1.45292 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00943 / 0.53 ( 3) link_ALPHA1-6 : angle 1.28713 / 0.71 ( 9) link_BETA1-4 : bond 0.00487 / 0.33 ( 36) link_BETA1-4 : angle 1.69700 / 1.14 ( 108) link_NAG-ASN : bond 0.00878 / 0.69 ( 63) link_NAG-ASN : angle 4.62300 / 3.47 ( 189) *********************** 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 280 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8444 (tt) cc_final: 0.8224 (tp) REVERT: A 233 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8260 (mm-40) REVERT: A 344 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: A 517 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7918 (tttp) REVERT: A 714 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: A 762 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8010 (ttp-110) REVERT: A 1069 LYS cc_start: 0.8113 (mtmp) cc_final: 0.7903 (mtpt) REVERT: A 1084 HIS cc_start: 0.8627 (m90) cc_final: 0.8323 (m90) REVERT: B 184 HIS cc_start: 0.6903 (m-70) cc_final: 0.6702 (m-70) REVERT: B 937 GLN cc_start: 0.8563 (mt0) cc_final: 0.7962 (pt0) REVERT: B 1002 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8484 (tpt170) REVERT: C 122 LEU cc_start: 0.8354 (tt) cc_final: 0.8108 (tp) REVERT: C 205 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.6685 (mmm160) REVERT: C 272 ASN cc_start: 0.7606 (m-40) cc_final: 0.7388 (m-40) REVERT: C 347 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7912 (ttt-90) REVERT: C 759 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7501 (ttm-80) outliers start: 66 outliers final: 30 residues processed: 249 average time/residue: 0.6218 time to fit residues: 181.7244 Evaluate side-chains 229 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 517 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain B residue 116 THR 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 947 LYS Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1117 ASN 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 624 VAL Chi-restraints excluded: chain C residue 675 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 981 THR Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 129 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 153 optimal weight: 40.0000 chunk 319 optimal weight: 1.9990 chunk 151 optimal weight: 0.0030 chunk 146 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 226 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 324 ASN A1102 ASN B 324 ASN B 988 GLN B1102 ASN C 135 ASN C 324 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126704 restraints weight = 29013.903| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.04 r_work: 0.3243 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2944 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= 0.112 Angle : 0.627 24.793 36328 Z= 0.297 Chirality : 0.048 0.642 4418 Planarity : 0.004 0.037 4525 Dihedral : 5.489 55.107 5449 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.54 % Allowed : 10.89 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3228 helix: 1.59 (0.20), residues: 735 sheet: 0.98 (0.19), residues: 744 loop : -0.85 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.020 0.001 TYR B1050 PHE 0.017 0.001 PHE B 665 TRP 0.015 0.001 TRP A 622 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (26308) covalent geometry : angle 0.53127 / 0.28 (35911) SS BOND : bond 0.00188 / 0.13 ( 42) SS BOND : angle 0.74740 / 0.48 ( 84) hydrogen bonds : bond 0.05285 / 3.68 ( 1010) hydrogen bonds : angle 5.11188 / 3.59 ( 2904) link_ALPHA1-2 : bond 0.00382 / 0.20 ( 3) link_ALPHA1-2 : angle 1.61982 / 0.88 ( 9) link_ALPHA1-3 : bond 0.01136 / 0.77 ( 6) link_ALPHA1-3 : angle 1.16608 / 0.82 ( 18) link_ALPHA1-6 : bond 0.01138 / 0.64 ( 3) link_ALPHA1-6 : angle 1.08649 / 0.60 ( 9) link_BETA1-4 : bond 0.00492 / 0.33 ( 36) link_BETA1-4 : angle 1.57300 / 1.07 ( 108) link_NAG-ASN : bond 0.00726 / 0.53 ( 63) link_NAG-ASN : angle 4.47180 / 3.29 ( 189) *********************** 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 250 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8136 (mm110) REVERT: A 517 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: A 714 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8392 (mtp) REVERT: A 759 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7591 (ttm-80) REVERT: A 762 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7959 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8586 (m90) cc_final: 0.8287 (m90) REVERT: B 165 TYR cc_start: 0.7475 (t80) cc_final: 0.7254 (t80) REVERT: B 899 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8326 (tt) REVERT: B 937 GLN cc_start: 0.8522 (mt0) cc_final: 0.8036 (pt0) REVERT: B 1102 ASN cc_start: 0.7860 (m-40) cc_final: 0.7572 (m110) REVERT: C 205 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.6617 (mmm160) REVERT: C 759 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7530 (ttm-80) outliers start: 37 outliers final: 11 residues processed: 230 average time/residue: 0.6264 time to fit residues: 169.1013 Evaluate side-chains 205 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 517 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 104 optimal weight: 0.5980 chunk 260 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 324 ASN A1054 GLN A1102 ASN B 135 ASN 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 = 0.3762 r_free = 0.3762 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124541 restraints weight = 29071.847| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.06 r_work: 0.3081 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26461 Z= 0.173 Angle : 0.673 22.326 36328 Z= 0.321 Chirality : 0.050 0.539 4418 Planarity : 0.004 0.039 4525 Dihedral : 5.727 55.381 5449 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.29 % Allowed : 10.43 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3228 helix: 1.51 (0.19), residues: 738 sheet: 1.02 (0.19), residues: 738 loop : -0.92 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 205 TYR 0.022 0.002 TYR C 484 PHE 0.017 0.002 PHE B1104 TRP 0.012 0.002 TRP A 622 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (26308) covalent geometry : angle 0.58156 / 0.30 (35911) SS BOND : bond 0.00252 / 0.18 ( 42) SS BOND : angle 1.12629 / 0.67 ( 84) hydrogen bonds : bond 0.06027 / 4.19 ( 1010) hydrogen bonds : angle 5.19693 / 3.65 ( 2904) link_ALPHA1-2 : bond 0.00177 / 0.10 ( 3) link_ALPHA1-2 : angle 1.58603 / 0.88 ( 9) link_ALPHA1-3 : bond 0.01015 / 0.66 ( 6) link_ALPHA1-3 : angle 1.40741 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00949 / 0.53 ( 3) link_ALPHA1-6 : angle 1.20101 / 0.66 ( 9) link_BETA1-4 : bond 0.00481 / 0.33 ( 36) link_BETA1-4 : angle 1.56979 / 1.06 ( 108) link_NAG-ASN : bond 0.00689 / 0.53 ( 63) link_NAG-ASN : angle 4.51172 / 3.28 ( 189) *********************** 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 256 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8911 (t0) REVERT: A 233 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8109 (mm110) REVERT: A 517 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7963 (mtpp) REVERT: A 714 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8355 (mtm) REVERT: A 759 ARG cc_start: 0.8036 (ttp-110) cc_final: 0.7492 (ttm-80) REVERT: A 762 ARG cc_start: 0.8299 (ttm110) cc_final: 0.8010 (ttp-110) REVERT: A 1002 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7914 (tpm170) REVERT: A 1084 HIS cc_start: 0.8614 (m90) cc_final: 0.8318 (m90) REVERT: B 165 TYR cc_start: 0.7509 (t80) cc_final: 0.7280 (t80) REVERT: B 184 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.6636 (m-70) REVERT: B 937 GLN cc_start: 0.8558 (mt0) cc_final: 0.8000 (pt0) REVERT: C 205 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.6500 (mmm160) REVERT: C 233 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7900 (mp-120) REVERT: C 347 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7868 (ttt-90) REVERT: C 759 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7470 (ttm-80) REVERT: C 1002 ARG cc_start: 0.8822 (tpt170) cc_final: 0.8566 (tpt170) outliers start: 55 outliers final: 28 residues processed: 232 average time/residue: 0.6121 time to fit residues: 166.7266 Evaluate side-chains 233 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN 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 490 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 1002 ARG 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 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 604 VAL 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 947 LYS Chi-restraints excluded: chain B residue 1117 ASN 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 325 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 408 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 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 279 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 324 ASN B 324 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 = 0.3765 r_free = 0.3765 target = 0.153647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124528 restraints weight = 28961.868| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.03 r_work: 0.3090 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3135 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= 0.148 Angle : 0.646 21.452 36328 Z= 0.309 Chirality : 0.049 0.583 4418 Planarity : 0.004 0.038 4525 Dihedral : 5.676 55.018 5449 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 10.47 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3228 helix: 1.60 (0.19), residues: 738 sheet: 1.02 (0.19), residues: 732 loop : -0.95 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.018 0.001 TYR C 484 PHE 0.021 0.002 PHE B 665 TRP 0.012 0.001 TRP A 622 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (26308) covalent geometry : angle 0.56003 / 0.29 (35911) SS BOND : bond 0.00226 / 0.17 ( 42) SS BOND : angle 0.96591 / 0.58 ( 84) hydrogen bonds : bond 0.05780 / 4.02 ( 1010) hydrogen bonds : angle 5.15630 / 3.63 ( 2904) link_ALPHA1-2 : bond 0.00221 / 0.12 ( 3) link_ALPHA1-2 : angle 1.59229 / 0.88 ( 9) link_ALPHA1-3 : bond 0.00994 / 0.67 ( 6) link_ALPHA1-3 : angle 1.33384 / 0.93 ( 18) link_ALPHA1-6 : bond 0.01084 / 0.61 ( 3) link_ALPHA1-6 : angle 1.23371 / 0.68 ( 9) link_BETA1-4 : bond 0.00450 / 0.30 ( 36) link_BETA1-4 : angle 1.53736 / 1.03 ( 108) link_NAG-ASN : bond 0.00699 / 0.54 ( 63) link_NAG-ASN : angle 4.30780 / 3.13 ( 189) *********************** 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 259 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8109 (mm110) REVERT: A 344 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: A 517 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7973 (mtpp) REVERT: A 714 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8347 (mtm) REVERT: A 759 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7572 (ttm-80) REVERT: A 762 ARG cc_start: 0.8282 (ttm110) cc_final: 0.8006 (ttp-110) REVERT: A 1002 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7909 (tpm170) REVERT: A 1084 HIS cc_start: 0.8638 (m90) cc_final: 0.8344 (m90) REVERT: B 165 TYR cc_start: 0.7499 (t80) cc_final: 0.7271 (t80) REVERT: B 883 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8697 (mtp) REVERT: B 937 GLN cc_start: 0.8546 (mt0) cc_final: 0.7996 (pt0) REVERT: C 205 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.6484 (mmm160) REVERT: C 233 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7862 (mp-120) REVERT: C 347 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7884 (ttt-90) REVERT: C 759 ARG cc_start: 0.7886 (ttp-170) cc_final: 0.7478 (ttm-80) REVERT: C 1002 ARG cc_start: 0.8782 (tpt170) cc_final: 0.8490 (tpt170) outliers start: 57 outliers final: 35 residues processed: 233 average time/residue: 0.6078 time to fit residues: 166.1772 Evaluate side-chains 230 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 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 899 LEU Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain B residue 116 THR 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 604 VAL 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 864 THR Chi-restraints excluded: chain B residue 883 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP 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 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 779 ASP Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 162 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 324 ASN B 324 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 = 0.3729 r_free = 0.3729 target = 0.150732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119801 restraints weight = 29447.514| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.22 r_work: 0.3198 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26461 Z= 0.153 Angle : 0.643 20.776 36328 Z= 0.310 Chirality : 0.048 0.484 4418 Planarity : 0.004 0.040 4525 Dihedral : 5.677 55.089 5449 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.42 % Allowed : 10.60 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3228 helix: 1.64 (0.19), residues: 738 sheet: 1.04 (0.19), residues: 756 loop : -1.02 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.018 0.001 TYR C 484 PHE 0.019 0.002 PHE A 665 TRP 0.012 0.002 TRP B 427 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (26308) covalent geometry : angle 0.56130 / 0.29 (35911) SS BOND : bond 0.00225 / 0.16 ( 42) SS BOND : angle 0.98043 / 0.60 ( 84) hydrogen bonds : bond 0.05801 / 4.03 ( 1010) hydrogen bonds : angle 5.14258 / 3.62 ( 2904) link_ALPHA1-2 : bond 0.00254 / 0.14 ( 3) link_ALPHA1-2 : angle 1.59562 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00960 / 0.65 ( 6) link_ALPHA1-3 : angle 1.36681 / 0.96 ( 18) link_ALPHA1-6 : bond 0.00942 / 0.54 ( 3) link_ALPHA1-6 : angle 1.18372 / 0.66 ( 9) link_BETA1-4 : bond 0.00464 / 0.31 ( 36) link_BETA1-4 : angle 1.55804 / 1.05 ( 108) link_NAG-ASN : bond 0.00758 / 0.58 ( 63) link_NAG-ASN : angle 4.18782 / 3.05 ( 189) *********************** 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 251 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8928 (t0) REVERT: A 233 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8076 (mm110) REVERT: A 344 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: A 517 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7966 (mtpp) REVERT: A 714 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: A 759 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7513 (ttm-80) REVERT: A 762 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7870 (ttp-110) REVERT: A 1002 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7842 (tpm170) REVERT: A 1084 HIS cc_start: 0.8611 (m90) cc_final: 0.8268 (m90) REVERT: B 165 TYR cc_start: 0.7539 (t80) cc_final: 0.7296 (t80) REVERT: B 304 GLN cc_start: 0.8145 (mp10) cc_final: 0.7721 (mm-40) REVERT: B 883 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8652 (mtp) REVERT: B 937 GLN cc_start: 0.8508 (mt0) cc_final: 0.7922 (pt0) REVERT: B 1069 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7638 (mtpp) REVERT: C 205 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.6537 (mmm160) REVERT: C 347 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7870 (ttt-90) REVERT: C 759 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7403 (ttm-80) outliers start: 58 outliers final: 38 residues processed: 226 average time/residue: 0.5669 time to fit residues: 150.9450 Evaluate side-chains 233 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 304 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 517 LYS Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain B residue 116 THR 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 517 LYS 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 779 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 883 MET Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1069 LYS Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 93 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 883 MET Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1117 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 301 optimal weight: 0.0370 chunk 134 optimal weight: 0.9980 chunk 315 optimal weight: 0.7980 chunk 259 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN B 324 ASN B 734 ASN B1102 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 = 0.3749 r_free = 0.3749 target = 0.152508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121659 restraints weight = 29442.308| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.26 r_work: 0.3185 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26461 Z= 0.116 Angle : 0.621 20.317 36328 Z= 0.296 Chirality : 0.047 0.454 4418 Planarity : 0.004 0.050 4525 Dihedral : 5.995 84.973 5449 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.54 % Allowed : 11.56 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3228 helix: 1.87 (0.20), residues: 738 sheet: 0.97 (0.19), residues: 738 loop : -0.92 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.019 0.001 TYR B1050 PHE 0.021 0.001 PHE C1104 TRP 0.012 0.001 TRP C 427 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (26308) covalent geometry : angle 0.53599 / 0.28 (35911) SS BOND : bond 0.00184 / 0.13 ( 42) SS BOND : angle 0.80033 / 0.49 ( 84) hydrogen bonds : bond 0.05167 / 3.59 ( 1010) hydrogen bonds : angle 4.99776 / 3.51 ( 2904) link_ALPHA1-2 : bond 0.00213 / 0.12 ( 3) link_ALPHA1-2 : angle 1.55808 / 0.86 ( 9) link_ALPHA1-3 : bond 0.01060 / 0.72 ( 6) link_ALPHA1-3 : angle 1.27840 / 0.90 ( 18) link_ALPHA1-6 : bond 0.01048 / 0.59 ( 3) link_ALPHA1-6 : angle 1.17766 / 0.65 ( 9) link_BETA1-4 : bond 0.00457 / 0.31 ( 36) link_BETA1-4 : angle 1.54231 / 1.04 ( 108) link_NAG-ASN : bond 0.00813 / 0.62 ( 63) link_NAG-ASN : angle 4.19863 / 3.07 ( 189) *********************** 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 237 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8061 (mm110) REVERT: A 517 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7950 (mtpp) REVERT: A 714 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: A 759 ARG cc_start: 0.8024 (ttp-110) cc_final: 0.7479 (ttm-80) REVERT: A 762 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7815 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8608 (m90) cc_final: 0.8265 (m90) REVERT: B 165 TYR cc_start: 0.7595 (t80) cc_final: 0.7382 (t80) REVERT: B 205 ARG cc_start: 0.7291 (ttm-80) cc_final: 0.6673 (mpt90) REVERT: B 304 GLN cc_start: 0.8119 (mp10) cc_final: 0.7693 (mm-40) REVERT: B 937 GLN cc_start: 0.8488 (mt0) cc_final: 0.7904 (pt0) REVERT: B 1069 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7587 (mtpp) REVERT: C 184 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6011 (m-70) REVERT: C 205 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7355 (ttm-80) REVERT: C 759 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7426 (ttm-80) outliers start: 37 outliers final: 22 residues processed: 221 average time/residue: 0.5885 time to fit residues: 153.1191 Evaluate side-chains 218 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 490 VAL 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 947 LYS Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP 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 844 LEU Chi-restraints excluded: chain C residue 947 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 145 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 324 ASN B 324 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 = 0.3732 r_free = 0.3732 target = 0.150966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119908 restraints weight = 29526.837| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.23 r_work: 0.3157 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26461 Z= 0.161 Angle : 0.661 20.018 36328 Z= 0.317 Chirality : 0.049 0.458 4418 Planarity : 0.004 0.052 4525 Dihedral : 6.129 87.736 5447 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.54 % Allowed : 11.81 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3228 helix: 1.70 (0.19), residues: 738 sheet: 1.00 (0.19), residues: 756 loop : -1.04 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.019 0.001 TYR C 484 PHE 0.021 0.002 PHE C1104 TRP 0.011 0.002 TRP B 427 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (26308) covalent geometry : angle 0.58106 / 0.30 (35911) SS BOND : bond 0.00230 / 0.17 ( 42) SS BOND : angle 0.97860 / 0.59 ( 84) hydrogen bonds : bond 0.05797 / 4.03 ( 1010) hydrogen bonds : angle 5.10108 / 3.58 ( 2904) link_ALPHA1-2 : bond 0.00181 / 0.10 ( 3) link_ALPHA1-2 : angle 1.55459 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00940 / 0.62 ( 6) link_ALPHA1-3 : angle 1.42044 / 0.99 ( 18) link_ALPHA1-6 : bond 0.00977 / 0.55 ( 3) link_ALPHA1-6 : angle 1.24339 / 0.69 ( 9) link_BETA1-4 : bond 0.00451 / 0.30 ( 36) link_BETA1-4 : angle 1.54766 / 1.04 ( 108) link_NAG-ASN : bond 0.00789 / 0.60 ( 63) link_NAG-ASN : angle 4.20103 / 3.05 ( 189) ********************** 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: 37 poor density : 192 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8990 (t0) REVERT: A 233 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8104 (mm110) REVERT: A 344 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: A 517 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: A 714 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8445 (mtp) REVERT: A 759 ARG cc_start: 0.8086 (ttp-110) cc_final: 0.7561 (ttm-80) REVERT: A 762 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7885 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8622 (m90) cc_final: 0.8296 (m90) REVERT: B 165 TYR cc_start: 0.7601 (t80) cc_final: 0.7383 (t80) REVERT: B 205 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.6844 (mpt90) REVERT: B 304 GLN cc_start: 0.8150 (mp10) cc_final: 0.7747 (mm-40) REVERT: B 809 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7785 (t) REVERT: B 937 GLN cc_start: 0.8523 (mt0) cc_final: 0.7972 (pt0) REVERT: B 1069 LYS cc_start: 0.7867 (mtpt) cc_final: 0.7649 (mtpp) REVERT: C 205 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.6496 (mmm160) REVERT: C 759 ARG cc_start: 0.7829 (ttp-170) cc_final: 0.7392 (ttm-80) outliers start: 37 outliers final: 28 residues processed: 214 average time/residue: 0.6037 time to fit residues: 152.4265 Evaluate side-chains 221 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 304 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 517 LYS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS 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 779 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 45 ASP 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 844 LEU Chi-restraints excluded: chain C residue 947 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 272 optimal weight: 0.3980 chunk 317 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 218 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 167 optimal weight: 0.1980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 324 ASN A1102 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 = 0.3736 r_free = 0.3736 target = 0.151339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120562 restraints weight = 29287.962| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.23 r_work: 0.3163 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 26461 Z= 0.151 Angle : 0.799 59.197 36328 Z= 0.407 Chirality : 0.051 0.895 4418 Planarity : 0.004 0.073 4525 Dihedral : 6.086 88.376 5447 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.75 % Allowed : 11.64 % Favored : 86.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3228 helix: 1.71 (0.19), residues: 738 sheet: 0.99 (0.19), residues: 756 loop : -1.05 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.018 0.001 TYR C 484 PHE 0.018 0.001 PHE C1104 TRP 0.011 0.001 TRP B 427 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (26308) covalent geometry : angle 0.71913 / 0.39 (35911) SS BOND : bond 0.00206 / 0.15 ( 42) SS BOND : angle 0.90360 / 0.55 ( 84) hydrogen bonds : bond 0.05679 / 3.95 ( 1010) hydrogen bonds : angle 5.09962 / 3.58 ( 2904) link_ALPHA1-2 : bond 0.00180 / 0.10 ( 3) link_ALPHA1-2 : angle 1.56291 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00883 / 0.57 ( 6) link_ALPHA1-3 : angle 1.46110 / 1.01 ( 18) link_ALPHA1-6 : bond 0.00876 / 0.50 ( 3) link_ALPHA1-6 : angle 1.20588 / 0.67 ( 9) link_BETA1-4 : bond 0.00435 / 0.29 ( 36) link_BETA1-4 : angle 1.54061 / 1.03 ( 108) link_NAG-ASN : bond 0.00853 / 0.66 ( 63) link_NAG-ASN : angle 4.71578 / 3.48 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8797.54 seconds wall clock time: 150 minutes 44.77 seconds (9044.77 seconds total)