Starting phenix.real_space_refine on Mon Aug 25 06:32:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u29_41842/08_2025/8u29_41842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u29_41842/08_2025/8u29_41842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u29_41842/08_2025/8u29_41842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u29_41842/08_2025/8u29_41842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u29_41842/08_2025/8u29_41842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u29_41842/08_2025/8u29_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-2.0-5787/lib/python3.9/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: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.61, per 1000 atoms: 0.26 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 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: 1.45 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: 7.41 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.50: 15841 1.50 - 1.84: 10464 1.84 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.87: 3 Bond restraints: 26308 Sorted by residual: bond pdb=" C PRO A 285 " pdb=" N LEU A 286 " ideal model delta sigma weight residual 1.335 2.866 -1.531 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C PRO B 285 " pdb=" N LEU B 286 " ideal model delta sigma weight residual 1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C PRO C 285 " pdb=" N LEU C 286 " ideal model delta sigma weight residual 1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04 bond pdb=" C ASN A 148 " pdb=" O ASN A 148 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.29e-02 6.01e+03 3.29e+01 bond pdb=" C ASN C 148 " pdb=" O ASN C 148 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.29e-02 6.01e+03 3.27e+01 ... (remaining 26303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.59: 35782 6.59 - 13.17: 120 13.17 - 19.76: 3 19.76 - 26.34: 3 26.34 - 32.93: 3 Bond angle restraints: 35911 Sorted by residual: angle pdb=" C PRO B 285 " pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta sigma weight residual 120.72 87.79 32.93 1.67e+00 3.59e-01 3.89e+02 angle pdb=" C PRO A 285 " pdb=" N LEU A 286 " pdb=" CA LEU A 286 " ideal model delta sigma weight residual 120.72 87.80 32.92 1.67e+00 3.59e-01 3.89e+02 angle pdb=" C PRO C 285 " pdb=" N LEU C 286 " pdb=" CA LEU C 286 " ideal model delta sigma weight residual 120.72 87.82 32.90 1.67e+00 3.59e-01 3.88e+02 angle pdb=" N HIS C 614 " pdb=" CA HIS C 614 " pdb=" CB HIS C 614 " ideal model delta sigma weight residual 110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02 angle pdb=" N HIS B 614 " pdb=" CA HIS B 614 " pdb=" CB HIS B 614 " ideal model delta sigma weight residual 110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02 ... (remaining 35906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 16286 21.62 - 43.25: 488 43.25 - 64.87: 105 64.87 - 86.49: 54 86.49 - 108.12: 30 Dihedral angle restraints: 16963 sinusoidal: 7501 harmonic: 9462 Sorted by residual: dihedral pdb=" C LEU A 613 " pdb=" N LEU A 613 " pdb=" CA LEU A 613 " pdb=" CB LEU A 613 " ideal model delta harmonic sigma weight residual -122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02 dihedral pdb=" C LEU C 613 " pdb=" N LEU C 613 " pdb=" CA LEU C 613 " pdb=" CB LEU C 613 " ideal model delta harmonic sigma weight residual -122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02 dihedral pdb=" C LEU B 613 " pdb=" N LEU B 613 " pdb=" CA LEU B 613 " pdb=" CB LEU B 613 " ideal model delta harmonic sigma weight residual -122.60 -161.92 39.32 0 2.50e+00 1.60e-01 2.47e+02 ... (remaining 16960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4391 0.340 - 0.680: 18 0.680 - 1.020: 0 1.020 - 1.360: 0 1.360 - 1.700: 9 Chirality restraints: 4418 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 148 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01 ... (remaining 4415 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO B 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO B 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU B 286 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO A 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO A 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU A 286 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C PRO C 285 " 0.175 2.00e-02 2.50e+03 pdb=" O PRO C 285 " -0.088 2.00e-02 2.50e+03 pdb=" N LEU C 286 " -0.032 2.00e-02 2.50e+03 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 12786 2.97 - 3.46: 22373 3.46 - 3.94: 42075 3.94 - 4.42: 47191 4.42 - 4.90: 77853 Nonbonded interactions: 202278 Sorted by model distance: nonbonded pdb=" O GLY B 891 " pdb=" NZ LYS B1021 " model vdw 2.492 3.120 nonbonded pdb=" O GLY C 891 " pdb=" NZ LYS C1021 " model vdw 2.492 3.120 nonbonded pdb=" O GLY A 891 " pdb=" NZ LYS A1021 " model vdw 2.492 3.120 nonbonded pdb=" OD1 ASP C 44 " pdb=" N ASP C 45 " model vdw 2.528 3.120 nonbonded pdb=" OD1 ASP A 44 " pdb=" N ASP A 45 " model vdw 2.528 3.120 ... (remaining 202273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 18 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 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: 12.360 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 28.740 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 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:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.531 26461 Z= 1.370 Angle : 1.448 32.925 36328 Z= 0.926 Chirality : 0.117 1.700 4418 Planarity : 0.006 0.103 4525 Dihedral : 12.485 108.116 10765 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.44 % Rotamer: Outliers : 1.13 % Allowed : 1.38 % Favored : 97.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.02007 (26308) covalent geometry : angle 1.41067 (35911) SS BOND : bond 0.05932 ( 42) SS BOND : angle 4.31341 ( 84) hydrogen bonds : bond 0.20295 ( 1010) hydrogen bonds : angle 7.67629 ( 2904) link_ALPHA1-2 : bond 0.06459 ( 3) link_ALPHA1-2 : angle 2.63285 ( 9) link_ALPHA1-3 : bond 0.06156 ( 6) link_ALPHA1-3 : angle 2.17215 ( 18) link_ALPHA1-6 : bond 0.04586 ( 3) link_ALPHA1-6 : angle 1.61410 ( 9) link_BETA1-4 : bond 0.05770 ( 36) link_BETA1-4 : angle 2.86244 ( 108) link_NAG-ASN : bond 0.05346 ( 63) link_NAG-ASN : angle 3.30307 ( 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 : 0.861 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: 0.6859 time to fit residues: 317.3991 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 : 0.677 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 201 HIS C 602 GLN C 787 GLN C 878 GLN C 918 GLN C 988 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121556 restraints weight = 29670.545| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.21 r_work: 0.3233 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26461 Z= 0.189 Angle : 0.729 28.372 36328 Z= 0.362 Chirality : 0.054 1.151 4418 Planarity : 0.005 0.038 4525 Dihedral : 9.764 93.862 5800 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.34 % Allowed : 7.93 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.14), residues: 3228 helix: 1.07 (0.20), residues: 753 sheet: 1.32 (0.19), residues: 669 loop : -0.54 (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 0.014 0.002 TRP C 622 HIS 0.011 0.002 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00429 (26308) covalent geometry : angle 0.65920 (35911) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.72460 ( 84) hydrogen bonds : bond 0.07033 ( 1010) hydrogen bonds : angle 5.75801 ( 2904) link_ALPHA1-2 : bond 0.00439 ( 3) link_ALPHA1-2 : angle 2.03746 ( 9) link_ALPHA1-3 : bond 0.01614 ( 6) link_ALPHA1-3 : angle 1.68710 ( 18) link_ALPHA1-6 : bond 0.01338 ( 3) link_ALPHA1-6 : angle 1.62094 ( 9) link_BETA1-4 : bond 0.00691 ( 36) link_BETA1-4 : angle 1.88751 ( 108) link_NAG-ASN : bond 0.00621 ( 63) link_NAG-ASN : angle 3.95078 ( 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 288 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 0.998 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: 0.8088 (tt) cc_final: 0.7709 (tp) REVERT: A 233 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8048 (mm110) REVERT: A 762 ARG cc_start: 0.7970 (ttm110) cc_final: 0.7661 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8550 (m90) cc_final: 0.8242 (m90) REVERT: A 1102 ASN cc_start: 0.6886 (m-40) cc_final: 0.6634 (m-40) REVERT: B 184 HIS cc_start: 0.6734 (m-70) cc_final: 0.5198 (p90) REVERT: B 759 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7289 (mtm-85) REVERT: B 1002 ARG cc_start: 0.8620 (tpt170) cc_final: 0.8348 (tpt170) REVERT: C 205 ARG cc_start: 0.7154 (ttm-80) cc_final: 0.6368 (mmm160) REVERT: C 595 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.6893 (mttt) outliers start: 56 outliers final: 14 residues processed: 257 average time/residue: 0.6278 time to fit residues: 188.3842 Evaluate side-chains 208 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 101 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 229 optimal weight: 0.1980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS A 304 GLN A 324 ASN A1054 GLN B 324 ASN B 436 GLN B1054 GLN C 324 ASN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118282 restraints weight = 29566.632| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.23 r_work: 0.3163 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26461 Z= 0.228 Angle : 0.765 25.398 36328 Z= 0.374 Chirality : 0.056 1.246 4418 Planarity : 0.005 0.040 4525 Dihedral : 8.876 90.595 5791 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.29 % Allowed : 9.18 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.14), residues: 3228 helix: 1.12 (0.20), residues: 732 sheet: 1.07 (0.19), residues: 687 loop : -0.81 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 205 TYR 0.030 0.002 TYR C 484 PHE 0.017 0.002 PHE B 123 TRP 0.014 0.002 TRP B 427 HIS 0.010 0.003 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00545 (26308) covalent geometry : angle 0.68820 (35911) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.91844 ( 84) hydrogen bonds : bond 0.07382 ( 1010) hydrogen bonds : angle 5.60650 ( 2904) link_ALPHA1-2 : bond 0.00129 ( 3) link_ALPHA1-2 : angle 2.14121 ( 9) link_ALPHA1-3 : bond 0.01457 ( 6) link_ALPHA1-3 : angle 1.08370 ( 18) link_ALPHA1-6 : bond 0.01393 ( 3) link_ALPHA1-6 : angle 1.17935 ( 9) link_BETA1-4 : bond 0.00668 ( 36) link_BETA1-4 : angle 1.71892 ( 108) link_NAG-ASN : bond 0.00568 ( 63) link_NAG-ASN : angle 4.34672 ( 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 273 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8418 (tt) cc_final: 0.8146 (tp) REVERT: A 233 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8259 (mm-40) REVERT: A 517 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7937 (tttp) REVERT: A 714 MET cc_start: 0.8784 (mtm) cc_final: 0.8561 (mtp) REVERT: A 762 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7851 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8623 (m90) cc_final: 0.8335 (m90) REVERT: B 184 HIS cc_start: 0.6694 (m-70) cc_final: 0.5464 (p90) REVERT: B 627 LEU cc_start: 0.7531 (mt) cc_final: 0.7321 (mm) REVERT: B 738 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8285 (mm-40) REVERT: B 759 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7536 (mtm-85) REVERT: B 937 GLN cc_start: 0.8474 (mt0) cc_final: 0.7808 (pt0) REVERT: B 1002 ARG cc_start: 0.8745 (tpt170) cc_final: 0.8423 (tpt170) REVERT: C 205 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.6633 (mmm160) REVERT: C 347 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7823 (ttt-90) REVERT: C 595 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.6980 (mttt) REVERT: C 738 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8448 (mm-40) REVERT: C 759 ARG cc_start: 0.7881 (ttp-170) cc_final: 0.7356 (ttm-80) outliers start: 55 outliers final: 27 residues processed: 245 average time/residue: 0.6629 time to fit residues: 189.9233 Evaluate side-chains 223 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 517 LYS 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 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 535 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 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 347 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 595 LYS 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 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: 0.9990 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 310 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 151 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 324 ASN A 602 GLN B 151 HIS B 324 ASN C 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123110 restraints weight = 29059.045| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.18 r_work: 0.3198 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26461 Z= 0.134 Angle : 0.656 24.887 36328 Z= 0.314 Chirality : 0.050 0.657 4418 Planarity : 0.004 0.036 4525 Dihedral : 8.060 85.734 5791 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.04 % Allowed : 10.10 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.14), residues: 3228 helix: 1.40 (0.20), residues: 732 sheet: 1.01 (0.19), residues: 738 loop : -0.81 (0.13), residues: 1758 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 0.012 0.001 TRP A 622 HIS 0.004 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00283 (26308) covalent geometry : angle 0.57787 (35911) SS BOND : bond 0.00224 ( 42) SS BOND : angle 1.27661 ( 84) hydrogen bonds : bond 0.05846 ( 1010) hydrogen bonds : angle 5.28000 ( 2904) link_ALPHA1-2 : bond 0.00134 ( 3) link_ALPHA1-2 : angle 1.85833 ( 9) link_ALPHA1-3 : bond 0.01497 ( 6) link_ALPHA1-3 : angle 1.21587 ( 18) link_ALPHA1-6 : bond 0.01560 ( 3) link_ALPHA1-6 : angle 1.10160 ( 9) link_BETA1-4 : bond 0.00539 ( 36) link_BETA1-4 : angle 1.62698 ( 108) link_NAG-ASN : bond 0.00794 ( 63) link_NAG-ASN : angle 4.08971 ( 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 263 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8351 (tt) cc_final: 0.8138 (tp) REVERT: A 233 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8025 (mm110) REVERT: A 714 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8367 (mtp) REVERT: A 759 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7310 (ttm-80) REVERT: A 762 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7902 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8570 (m90) cc_final: 0.8270 (m90) REVERT: A 1102 ASN cc_start: 0.7533 (m-40) cc_final: 0.6972 (m110) REVERT: B 165 TYR cc_start: 0.7565 (t80) cc_final: 0.7334 (t80) REVERT: B 205 ARG cc_start: 0.7232 (ttm-80) cc_final: 0.6761 (mmm160) REVERT: B 759 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7192 (ttm-80) REVERT: B 937 GLN cc_start: 0.8460 (mt0) cc_final: 0.7840 (pt0) REVERT: C 122 LEU cc_start: 0.8200 (tt) cc_final: 0.7957 (tp) REVERT: C 205 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.6623 (mmm160) REVERT: C 347 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7792 (ttt-90) REVERT: C 759 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7309 (ttm-80) outliers start: 49 outliers final: 18 residues processed: 235 average time/residue: 0.6312 time to fit residues: 173.5521 Evaluate side-chains 208 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 714 MET Chi-restraints excluded: chain A residue 947 LYS 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 490 VAL Chi-restraints excluded: chain B residue 517 LYS 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 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 883 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 153 optimal weight: 40.0000 chunk 319 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 146 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 324 ASN B 135 ASN B 324 ASN C 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121937 restraints weight = 29126.582| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.19 r_work: 0.3204 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26461 Z= 0.128 Angle : 0.627 22.648 36328 Z= 0.301 Chirality : 0.049 0.526 4418 Planarity : 0.004 0.037 4525 Dihedral : 7.584 83.303 5789 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.09 % Allowed : 10.76 % 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 aren not related in a simple way. whole: 0.27 (0.14), residues: 3228 helix: 1.59 (0.20), residues: 735 sheet: 1.00 (0.19), residues: 744 loop : -0.82 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.019 0.001 TYR B1050 PHE 0.023 0.001 PHE B1104 TRP 0.011 0.001 TRP A 622 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00276 (26308) covalent geometry : angle 0.54832 (35911) SS BOND : bond 0.00233 ( 42) SS BOND : angle 1.19859 ( 84) hydrogen bonds : bond 0.05536 ( 1010) hydrogen bonds : angle 5.13026 ( 2904) link_ALPHA1-2 : bond 0.00133 ( 3) link_ALPHA1-2 : angle 1.79674 ( 9) link_ALPHA1-3 : bond 0.01347 ( 6) link_ALPHA1-3 : angle 1.16332 ( 18) link_ALPHA1-6 : bond 0.01519 ( 3) link_ALPHA1-6 : angle 1.11878 ( 9) link_BETA1-4 : bond 0.00515 ( 36) link_BETA1-4 : angle 1.53752 ( 108) link_NAG-ASN : bond 0.00722 ( 63) link_NAG-ASN : angle 4.00312 ( 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 252 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8050 (mm110) REVERT: A 714 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8395 (mtp) REVERT: A 759 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7318 (ttm-80) REVERT: A 762 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7841 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8612 (m90) cc_final: 0.8304 (m90) REVERT: A 1102 ASN cc_start: 0.7555 (m-40) cc_final: 0.7093 (m110) REVERT: B 165 TYR cc_start: 0.7595 (t80) cc_final: 0.7360 (t80) REVERT: B 205 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.6787 (mmm160) REVERT: B 759 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7189 (ttm-80) REVERT: B 937 GLN cc_start: 0.8442 (mt0) cc_final: 0.7847 (pt0) REVERT: C 122 LEU cc_start: 0.8177 (tt) cc_final: 0.7947 (tp) REVERT: C 205 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.6537 (mmm160) REVERT: C 347 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7810 (ttt-90) REVERT: C 759 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7369 (ttm-80) outliers start: 50 outliers final: 23 residues processed: 228 average time/residue: 0.6493 time to fit residues: 172.4987 Evaluate side-chains 212 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 759 ARG 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 184 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 883 MET 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: 2.9990 chunk 283 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 83 optimal weight: 0.1980 chunk 104 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 135 ASN A 184 HIS A 304 GLN A 324 ASN A 918 GLN B 135 ASN B 324 ASN C 135 ASN C 324 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117215 restraints weight = 29518.966| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.19 r_work: 0.3133 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 26461 Z= 0.252 Angle : 0.746 21.493 36328 Z= 0.362 Chirality : 0.054 0.524 4418 Planarity : 0.005 0.044 4525 Dihedral : 8.095 85.499 5789 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.71 % Allowed : 10.26 % Favored : 87.03 % 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 aren not related in a simple way. whole: -0.04 (0.14), residues: 3228 helix: 1.18 (0.19), residues: 738 sheet: 1.00 (0.19), residues: 762 loop : -1.07 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 455 TYR 0.027 0.002 TYR C 484 PHE 0.018 0.002 PHE A 665 TRP 0.013 0.002 TRP A 427 HIS 0.009 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00618 (26308) covalent geometry : angle 0.67229 (35911) SS BOND : bond 0.00335 ( 42) SS BOND : angle 1.63835 ( 84) hydrogen bonds : bond 0.07099 ( 1010) hydrogen bonds : angle 5.45620 ( 2904) link_ALPHA1-2 : bond 0.00085 ( 3) link_ALPHA1-2 : angle 1.86567 ( 9) link_ALPHA1-3 : bond 0.01191 ( 6) link_ALPHA1-3 : angle 1.45152 ( 18) link_ALPHA1-6 : bond 0.01330 ( 3) link_ALPHA1-6 : angle 1.24579 ( 9) link_BETA1-4 : bond 0.00524 ( 36) link_BETA1-4 : angle 1.65558 ( 108) link_NAG-ASN : bond 0.00673 ( 63) link_NAG-ASN : angle 4.24265 ( 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 265 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8908 (t0) REVERT: A 233 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8239 (mm-40) REVERT: A 344 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: A 714 MET cc_start: 0.8754 (mtm) cc_final: 0.8519 (mtp) REVERT: A 762 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7878 (ttp-110) REVERT: A 973 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6929 (mm-30) REVERT: A 1002 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8229 (tpm170) REVERT: A 1084 HIS cc_start: 0.8625 (m90) cc_final: 0.8329 (m90) REVERT: B 165 TYR cc_start: 0.7637 (t80) cc_final: 0.7386 (t80) REVERT: B 205 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.6777 (mmm160) REVERT: B 759 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7548 (mtm-85) REVERT: B 937 GLN cc_start: 0.8456 (mt0) cc_final: 0.7838 (pt0) REVERT: C 122 LEU cc_start: 0.8401 (tt) cc_final: 0.8164 (tp) REVERT: C 205 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.6545 (mmm160) REVERT: C 272 ASN cc_start: 0.7579 (m-40) cc_final: 0.7374 (m-40) REVERT: C 347 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7813 (ttt-90) outliers start: 65 outliers final: 36 residues processed: 240 average time/residue: 0.6272 time to fit residues: 176.9299 Evaluate side-chains 233 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 344 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 743 CYS 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 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 759 ARG Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 864 THR 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 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 905 GLN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 279 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 223 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 184 HIS A 324 ASN B 324 ASN B1102 ASN C 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119394 restraints weight = 29355.784| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.24 r_work: 0.3176 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26461 Z= 0.134 Angle : 0.637 20.829 36328 Z= 0.307 Chirality : 0.049 0.521 4418 Planarity : 0.004 0.039 4525 Dihedral : 7.688 82.209 5789 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.75 % Allowed : 11.39 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3228 helix: 1.51 (0.19), residues: 738 sheet: 1.05 (0.19), residues: 756 loop : -1.03 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.019 0.001 TYR B1050 PHE 0.025 0.001 PHE B 665 TRP 0.013 0.001 TRP A 622 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00293 (26308) covalent geometry : angle 0.56270 (35911) SS BOND : bond 0.00241 ( 42) SS BOND : angle 1.20594 ( 84) hydrogen bonds : bond 0.05748 ( 1010) hydrogen bonds : angle 5.19559 ( 2904) link_ALPHA1-2 : bond 0.00141 ( 3) link_ALPHA1-2 : angle 1.80053 ( 9) link_ALPHA1-3 : bond 0.01407 ( 6) link_ALPHA1-3 : angle 1.24206 ( 18) link_ALPHA1-6 : bond 0.01508 ( 3) link_ALPHA1-6 : angle 1.02279 ( 9) link_BETA1-4 : bond 0.00486 ( 36) link_BETA1-4 : angle 1.57930 ( 108) link_NAG-ASN : bond 0.00668 ( 63) link_NAG-ASN : angle 3.93014 ( 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 237 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8935 (t0) REVERT: A 233 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8025 (mm110) REVERT: A 344 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: A 714 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8381 (mtp) REVERT: A 759 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7407 (ttm-80) REVERT: A 762 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7890 (ttp-110) REVERT: A 1084 HIS cc_start: 0.8614 (m90) cc_final: 0.8297 (m90) REVERT: B 165 TYR cc_start: 0.7644 (t80) cc_final: 0.7417 (t80) REVERT: B 184 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.6170 (m170) REVERT: B 205 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.7090 (ttm-80) REVERT: B 304 GLN cc_start: 0.8117 (mp10) cc_final: 0.7671 (mm-40) REVERT: B 759 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7488 (mtm-85) REVERT: B 937 GLN cc_start: 0.8446 (mt0) cc_final: 0.7845 (pt0) REVERT: B 1102 ASN cc_start: 0.8214 (m-40) cc_final: 0.7998 (m110) REVERT: C 205 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.6443 (mmm160) REVERT: C 347 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7829 (ttt-90) REVERT: C 759 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7316 (ttm-80) outliers start: 42 outliers final: 24 residues processed: 215 average time/residue: 0.6046 time to fit residues: 151.9702 Evaluate side-chains 213 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 344 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 714 MET 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 315 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 759 ARG 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 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 688 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 162 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 127 optimal weight: 0.0470 chunk 17 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 184 HIS A 324 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 = 0.151277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119501 restraints weight = 29381.341| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.33 r_work: 0.3184 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26461 Z= 0.131 Angle : 0.621 20.449 36328 Z= 0.301 Chirality : 0.048 0.452 4418 Planarity : 0.004 0.038 4525 Dihedral : 7.455 80.299 5789 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.17 % Allowed : 11.14 % Favored : 86.69 % 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 aren not related in a simple way. whole: 0.21 (0.14), residues: 3228 helix: 1.68 (0.20), residues: 738 sheet: 1.01 (0.19), residues: 732 loop : -0.96 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.018 0.001 TYR B1050 PHE 0.020 0.001 PHE B 665 TRP 0.012 0.001 TRP A 622 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00288 (26308) covalent geometry : angle 0.54774 (35911) SS BOND : bond 0.00225 ( 42) SS BOND : angle 1.09449 ( 84) hydrogen bonds : bond 0.05509 ( 1010) hydrogen bonds : angle 5.10159 ( 2904) link_ALPHA1-2 : bond 0.00152 ( 3) link_ALPHA1-2 : angle 1.74276 ( 9) link_ALPHA1-3 : bond 0.01370 ( 6) link_ALPHA1-3 : angle 1.18855 ( 18) link_ALPHA1-6 : bond 0.01494 ( 3) link_ALPHA1-6 : angle 1.05259 ( 9) link_BETA1-4 : bond 0.00483 ( 36) link_BETA1-4 : angle 1.55406 ( 108) link_NAG-ASN : bond 0.00760 ( 63) link_NAG-ASN : angle 3.84742 ( 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 246 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8829 (t0) REVERT: A 233 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7852 (mm110) REVERT: A 344 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: A 714 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8311 (mtp) REVERT: A 759 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7120 (ttm-80) REVERT: A 762 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7532 (ttp-110) REVERT: A 1002 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7618 (tpm170) REVERT: A 1084 HIS cc_start: 0.8559 (m90) cc_final: 0.8265 (m90) REVERT: A 1102 ASN cc_start: 0.7868 (m-40) cc_final: 0.7643 (m-40) REVERT: B 165 TYR cc_start: 0.7566 (t80) cc_final: 0.7331 (t80) REVERT: B 184 HIS cc_start: 0.6753 (OUTLIER) cc_final: 0.5976 (m170) REVERT: B 304 GLN cc_start: 0.8054 (mp10) cc_final: 0.7491 (mm-40) REVERT: B 937 GLN cc_start: 0.8338 (mt0) cc_final: 0.7592 (pt0) REVERT: B 1102 ASN cc_start: 0.8066 (m-40) cc_final: 0.7822 (m-40) REVERT: C 205 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.6316 (mmm160) REVERT: C 347 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7664 (ttt-90) REVERT: C 759 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.6905 (ttm-80) outliers start: 52 outliers final: 30 residues processed: 226 average time/residue: 0.6023 time to fit residues: 159.9001 Evaluate side-chains 219 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR 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 595 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 779 ASP 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 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 688 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 162 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 315 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 184 HIS A 324 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 = 0.3718 r_free = 0.3718 target = 0.149643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117355 restraints weight = 29509.190| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.32 r_work: 0.3152 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26461 Z= 0.178 Angle : 0.668 20.189 36328 Z= 0.322 Chirality : 0.050 0.480 4418 Planarity : 0.004 0.051 4525 Dihedral : 7.801 80.612 5789 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.13 % Allowed : 11.31 % Favored : 86.57 % 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 aren not related in a simple way. whole: 0.08 (0.14), residues: 3228 helix: 1.54 (0.19), residues: 738 sheet: 0.97 (0.19), residues: 732 loop : -1.05 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.021 0.002 TYR C 484 PHE 0.025 0.002 PHE A 665 TRP 0.011 0.002 TRP B 427 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00422 (26308) covalent geometry : angle 0.59524 (35911) SS BOND : bond 0.00257 ( 42) SS BOND : angle 1.15687 ( 84) hydrogen bonds : bond 0.06051 ( 1010) hydrogen bonds : angle 5.19421 ( 2904) link_ALPHA1-2 : bond 0.00140 ( 3) link_ALPHA1-2 : angle 1.75709 ( 9) link_ALPHA1-3 : bond 0.01253 ( 6) link_ALPHA1-3 : angle 1.26733 ( 18) link_ALPHA1-6 : bond 0.01420 ( 3) link_ALPHA1-6 : angle 1.10715 ( 9) link_BETA1-4 : bond 0.00484 ( 36) link_BETA1-4 : angle 1.56953 ( 108) link_NAG-ASN : bond 0.00743 ( 63) link_NAG-ASN : angle 4.02437 ( 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 236 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8893 (t0) REVERT: A 233 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7893 (mm110) REVERT: A 344 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: A 714 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8347 (mtp) REVERT: A 759 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7126 (ttm-80) REVERT: A 762 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7649 (ttp-110) REVERT: A 1002 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7624 (tpm170) REVERT: A 1084 HIS cc_start: 0.8591 (m90) cc_final: 0.8280 (m90) REVERT: B 165 TYR cc_start: 0.7597 (t80) cc_final: 0.7373 (t80) REVERT: B 184 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6018 (m170) REVERT: B 304 GLN cc_start: 0.8065 (mp10) cc_final: 0.7522 (mm-40) REVERT: B 937 GLN cc_start: 0.8384 (mt0) cc_final: 0.7653 (pt0) REVERT: B 1102 ASN cc_start: 0.8225 (m-40) cc_final: 0.8007 (m110) REVERT: C 205 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.6404 (mmm160) REVERT: C 347 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7701 (ttt-90) REVERT: C 759 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7022 (ttm-80) outliers start: 51 outliers final: 36 residues processed: 216 average time/residue: 0.6140 time to fit residues: 154.1572 Evaluate side-chains 218 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR 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 595 LYS Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1117 ASN 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 315 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 864 THR 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 45 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 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 688 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 145 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 278 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 184 HIS A 324 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 = 0.3730 r_free = 0.3730 target = 0.150804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119032 restraints weight = 29585.742| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.34 r_work: 0.3172 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26461 Z= 0.136 Angle : 0.635 20.023 36328 Z= 0.306 Chirality : 0.048 0.435 4418 Planarity : 0.004 0.052 4525 Dihedral : 7.664 88.250 5789 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.79 % Allowed : 12.06 % Favored : 86.15 % 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 aren not related in a simple way. whole: 0.15 (0.14), residues: 3228 helix: 1.69 (0.20), residues: 738 sheet: 0.97 (0.19), residues: 732 loop : -1.02 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.018 0.001 TYR B1050 PHE 0.023 0.001 PHE B 665 TRP 0.012 0.001 TRP A 622 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00304 (26308) covalent geometry : angle 0.56274 (35911) SS BOND : bond 0.00217 ( 42) SS BOND : angle 0.95931 ( 84) hydrogen bonds : bond 0.05579 ( 1010) hydrogen bonds : angle 5.09665 ( 2904) link_ALPHA1-2 : bond 0.00162 ( 3) link_ALPHA1-2 : angle 1.73070 ( 9) link_ALPHA1-3 : bond 0.01319 ( 6) link_ALPHA1-3 : angle 1.18831 ( 18) link_ALPHA1-6 : bond 0.01484 ( 3) link_ALPHA1-6 : angle 1.03665 ( 9) link_BETA1-4 : bond 0.00478 ( 36) link_BETA1-4 : angle 1.56225 ( 108) link_NAG-ASN : bond 0.00729 ( 63) link_NAG-ASN : angle 3.90213 ( 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 231 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8866 (t0) REVERT: A 233 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7894 (mm110) REVERT: A 344 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: A 714 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8328 (mtp) REVERT: A 759 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7109 (ttm-80) REVERT: A 762 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7596 (ttp-110) REVERT: A 1002 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7582 (tpm170) REVERT: A 1084 HIS cc_start: 0.8572 (m90) cc_final: 0.8233 (m90) REVERT: A 1102 ASN cc_start: 0.8020 (m-40) cc_final: 0.7813 (m-40) REVERT: B 165 TYR cc_start: 0.7603 (t80) cc_final: 0.7353 (t80) REVERT: B 184 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.6074 (m170) REVERT: B 205 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.6585 (mpt90) REVERT: B 304 GLN cc_start: 0.8074 (mp10) cc_final: 0.7523 (mm-40) REVERT: B 809 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7582 (t) REVERT: B 937 GLN cc_start: 0.8370 (mt0) cc_final: 0.7644 (pt0) REVERT: B 1102 ASN cc_start: 0.8120 (m-40) cc_final: 0.7916 (m110) REVERT: C 205 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.6381 (mmm160) REVERT: C 347 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7658 (ttt-90) REVERT: C 759 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.6995 (ttm-80) outliers start: 43 outliers final: 32 residues processed: 214 average time/residue: 0.6151 time to fit residues: 154.0709 Evaluate side-chains 224 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR 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 714 MET Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1117 ASN 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 315 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 809 VAL 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 45 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 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 688 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 272 optimal weight: 1.9990 chunk 317 optimal weight: 0.0570 chunk 196 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 167 optimal weight: 0.0970 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 324 ASN B 324 ASN B 988 GLN C 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119848 restraints weight = 29341.118| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.30 r_work: 0.3193 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26461 Z= 0.119 Angle : 0.611 19.881 36328 Z= 0.295 Chirality : 0.047 0.420 4418 Planarity : 0.004 0.051 4525 Dihedral : 7.634 93.303 5789 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.75 % Allowed : 11.97 % Favored : 86.27 % 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 aren not related in a simple way. whole: 0.20 (0.14), residues: 3228 helix: 1.81 (0.20), residues: 738 sheet: 0.94 (0.19), residues: 738 loop : -1.00 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.019 0.001 TYR B1050 PHE 0.020 0.001 PHE C1104 TRP 0.011 0.001 TRP B 427 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00252 (26308) covalent geometry : angle 0.54040 (35911) SS BOND : bond 0.00198 ( 42) SS BOND : angle 0.85218 ( 84) hydrogen bonds : bond 0.05213 ( 1010) hydrogen bonds : angle 5.00072 ( 2904) link_ALPHA1-2 : bond 0.00185 ( 3) link_ALPHA1-2 : angle 1.68495 ( 9) link_ALPHA1-3 : bond 0.01316 ( 6) link_ALPHA1-3 : angle 1.13502 ( 18) link_ALPHA1-6 : bond 0.01512 ( 3) link_ALPHA1-6 : angle 1.00620 ( 9) link_BETA1-4 : bond 0.00471 ( 36) link_BETA1-4 : angle 1.52810 ( 108) link_NAG-ASN : bond 0.00680 ( 63) link_NAG-ASN : angle 3.77194 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9280.60 seconds wall clock time: 158 minutes 33.19 seconds (9513.19 seconds total)