Starting phenix.real_space_refine on Fri Jun 20 00:22:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2p_25621/06_2025/7t2p_25621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2p_25621/06_2025/7t2p_25621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t2p_25621/06_2025/7t2p_25621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2p_25621/06_2025/7t2p_25621.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2p_25621/06_2025/7t2p_25621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2p_25621/06_2025/7t2p_25621.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.049 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 147 5.16 5 C 14283 2.51 5 N 3693 2.21 5 O 4773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22896 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "B" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "R" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "1" 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: "2" 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: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" 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: "5" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "7" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "8" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "9" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" 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: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "7" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 13.78, per 1000 atoms: 0.60 Number of scatterers: 22896 At special positions: 0 Unit cell: (154.1, 156.4, 121.9, 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 147 16.00 O 4773 8.00 N 3693 7.00 C 14283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 211 " distance=1.78 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 168 " distance=2.02 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 263 " distance=2.04 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 255 " distance=2.05 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 459 " distance=2.03 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS H 100C" - pdb=" SG CYS H 100K" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 108 " - pdb=" SG CYS Q 211 " distance=1.78 Simple disulfide: pdb=" SG CYS Q 113 " - pdb=" SG CYS Q 168 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 194 " - pdb=" SG CYS Q 206 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 233 " - pdb=" SG CYS Q 263 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 243 " - pdb=" SG CYS Q 255 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 311 " - pdb=" SG CYS Q 344 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 395 " - pdb=" SG CYS Q 459 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 402 " - pdb=" SG CYS Q 432 " distance=2.02 Simple disulfide: pdb=" SG CYS S 100C" - pdb=" SG CYS S 100K" distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 101 " - pdb=" SG CYS 6 220 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 108 " - pdb=" SG CYS 6 211 " distance=1.78 Simple disulfide: pdb=" SG CYS 6 113 " - pdb=" SG CYS 6 168 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 194 " - pdb=" SG CYS 6 206 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 233 " - pdb=" SG CYS 6 263 " distance=2.04 Simple disulfide: pdb=" SG CYS 6 243 " - pdb=" SG CYS 6 255 " distance=2.05 Simple disulfide: pdb=" SG CYS 6 311 " - pdb=" SG CYS 6 344 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 395 " - pdb=" SG CYS 6 459 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 402 " - pdb=" SG CYS 6 432 " distance=2.02 Simple disulfide: pdb=" SG CYS 8 100C" - pdb=" SG CYS 8 100K" distance=2.03 Simple disulfide: pdb=" SG CYS 9 23 " - pdb=" SG CYS 9 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN C 5 " - " MAN C 6 " " MAN I 4 " - " MAN I 5 " " MAN U 5 " - " MAN U 6 " " MAN Z 4 " - " MAN Z 5 " " MAN a 5 " - " MAN a 6 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA C 3 " - " MAN C 8 " " MAN C 4 " - " MAN C 5 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 8 " " MAN a 4 " - " MAN a 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 7 " " BMA I 3 " - " MAN I 6 " " BMA J 3 " - " MAN J 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 7 " " BMA Z 3 " - " MAN Z 6 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 7 " " BMA f 3 " - " MAN f 6 " " BMA g 3 " - " MAN g 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " " NAG G 1 " - " FUC G 3 " " NAG W 1 " - " FUC W 3 " " NAG X 1 " - " FUC X 3 " " NAG Y 1 " - " FUC Y 3 " " NAG c 1 " - " FUC c 3 " " NAG d 1 " - " FUC d 3 " " NAG e 1 " - " FUC e 3 " NAG-ASN " NAG 0 1 " - " ASN Q 284 " " NAG 1 1 " - " ASN Q 295 " " NAG 2 1 " - " ASN Q 316 " " NAG 3 1 " - " ASN Q 377 " " NAG 4 1 " - " ASN Q 460 " " NAG 5 1 " - " ASN Q 479 " " NAG 6 601 " - " ASN 6 70 " " NAG 6 602 " - " ASN 6 79 " " NAG 6 603 " - " ASN 6 171 " " NAG 6 604 " - " ASN 6 184 " " NAG 6 605 " - " ASN 6 198 " " NAG 6 606 " - " ASN 6 202 " " NAG 6 607 " - " ASN 6 244 " " NAG 6 608 " - " ASN 6 306 " " NAG 6 609 " - " ASN 6 476 " " NAG 6 610 " - " ASN 6 371 " " NAG 7 701 " - " ASN 7 627 " " NAG 7 702 " - " ASN 7 636 " " NAG 7 703 " - " ASN 7 652 " " NAG A 601 " - " ASN A 70 " " NAG A 602 " - " ASN A 79 " " NAG A 603 " - " ASN A 171 " " NAG A 604 " - " ASN A 184 " " NAG A 605 " - " ASN A 198 " " NAG A 606 " - " ASN A 202 " " NAG A 607 " - " ASN A 244 " " NAG A 608 " - " ASN A 306 " " NAG A 609 " - " ASN A 476 " " NAG A 610 " - " ASN A 371 " " NAG B 701 " - " ASN B 627 " " NAG B 702 " - " ASN B 636 " " NAG B 703 " - " ASN B 652 " " NAG C 1 " - " ASN A 37 " " NAG D 1 " - " ASN A 114 " " NAG E 1 " - " ASN A 146 " " NAG F 1 " - " ASN A 156 " " NAG G 1 " - " ASN A 212 " " NAG I 1 " - " ASN A 278 " " NAG J 1 " - " ASN A 284 " " NAG K 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 316 " " NAG N 1 " - " ASN A 377 " " NAG O 1 " - " ASN A 460 " " NAG P 1 " - " ASN A 479 " " NAG Q 601 " - " ASN Q 70 " " NAG Q 602 " - " ASN Q 79 " " NAG Q 603 " - " ASN Q 171 " " NAG Q 604 " - " ASN Q 184 " " NAG Q 605 " - " ASN Q 198 " " NAG Q 606 " - " ASN Q 202 " " NAG Q 607 " - " ASN Q 244 " " NAG Q 608 " - " ASN Q 306 " " NAG Q 609 " - " ASN Q 476 " " NAG Q 610 " - " ASN Q 371 " " NAG R 701 " - " ASN R 627 " " NAG R 702 " - " ASN R 636 " " NAG R 703 " - " ASN R 652 " " NAG U 1 " - " ASN Q 37 " " NAG V 1 " - " ASN Q 114 " " NAG W 1 " - " ASN Q 146 " " NAG X 1 " - " ASN Q 156 " " NAG Y 1 " - " ASN Q 212 " " NAG Z 1 " - " ASN Q 278 " " NAG a 1 " - " ASN 6 37 " " NAG b 1 " - " ASN 6 114 " " NAG c 1 " - " ASN 6 146 " " NAG d 1 " - " ASN 6 156 " " NAG e 1 " - " ASN 6 212 " " NAG f 1 " - " ASN 6 278 " " NAG g 1 " - " ASN 6 284 " " NAG h 1 " - " ASN 6 295 " " NAG i 1 " - " ASN 6 316 " " NAG j 1 " - " ASN 6 377 " " NAG k 1 " - " ASN 6 460 " " NAG l 1 " - " ASN 6 479 " TRANS " SER 8 52 " - " TYR 8 52A" " TYR 8 52A" - " ILE 8 51 " " ASP 8 53 " - " SER 8 52 " " SER H 52 " - " TYR H 52A" " TYR H 52A" - " ILE H 51 " " ASP H 53 " - " SER H 52 " " SER S 52 " - " TYR S 52A" " TYR S 52A" - " ILE S 51 " " ASP S 53 " - " SER S 52 " Time building additional restraints: 7.81 Conformation dependent library (CDL) restraints added in 2.5 seconds 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 23.5% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.659A pdb=" N ILE A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 553 through 573 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 585 through 612 Processing helix chain 'B' and resid 638 through 644 removed outlier: 4.069A pdb=" N ARG B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 674 removed outlier: 4.093A pdb=" N GLU B 651 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN B 652 " --> pdb=" O PHE B 648 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'Q' and resid 51 through 57 Processing helix chain 'Q' and resid 81 through 99 Processing helix chain 'Q' and resid 104 through 108 Processing helix chain 'Q' and resid 114 through 121 Processing helix chain 'Q' and resid 149 through 154 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 302 through 306 Processing helix chain 'Q' and resid 349 through 363 Processing helix chain 'Q' and resid 372 through 376 removed outlier: 3.659A pdb=" N ILE Q 376 " --> pdb=" O THR Q 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 385 through 390 Processing helix chain 'Q' and resid 404 through 412 Processing helix chain 'Q' and resid 420 through 424 Processing helix chain 'Q' and resid 485 through 488 Processing helix chain 'Q' and resid 489 through 494 Processing helix chain 'R' and resid 537 through 541 Processing helix chain 'R' and resid 553 through 573 Processing helix chain 'R' and resid 574 through 576 No H-bonds generated for 'chain 'R' and resid 574 through 576' Processing helix chain 'R' and resid 585 through 612 Processing helix chain 'R' and resid 638 through 644 removed outlier: 4.068A pdb=" N ARG R 644 " --> pdb=" O GLN R 640 " (cutoff:3.500A) Processing helix chain 'R' and resid 646 through 674 removed outlier: 4.093A pdb=" N GLU R 651 " --> pdb=" O ASP R 647 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN R 652 " --> pdb=" O PHE R 648 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA R 655 " --> pdb=" O GLU R 651 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain '6' and resid 51 through 57 Processing helix chain '6' and resid 81 through 99 Processing helix chain '6' and resid 104 through 108 Processing helix chain '6' and resid 114 through 121 Processing helix chain '6' and resid 149 through 154 Processing helix chain '6' and resid 190 through 192 No H-bonds generated for 'chain '6' and resid 190 through 192' Processing helix chain '6' and resid 302 through 306 Processing helix chain '6' and resid 349 through 363 Processing helix chain '6' and resid 372 through 376 removed outlier: 3.658A pdb=" N ILE 6 376 " --> pdb=" O THR 6 373 " (cutoff:3.500A) Processing helix chain '6' and resid 385 through 390 Processing helix chain '6' and resid 404 through 412 Processing helix chain '6' and resid 420 through 424 Processing helix chain '6' and resid 485 through 488 Processing helix chain '6' and resid 489 through 494 Processing helix chain '7' and resid 537 through 541 Processing helix chain '7' and resid 553 through 573 Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 585 through 612 Processing helix chain '7' and resid 638 through 644 removed outlier: 4.069A pdb=" N ARG 7 644 " --> pdb=" O GLN 7 640 " (cutoff:3.500A) Processing helix chain '7' and resid 646 through 674 removed outlier: 4.093A pdb=" N GLU 7 651 " --> pdb=" O ASP 7 647 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN 7 652 " --> pdb=" O PHE 7 648 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA 7 655 " --> pdb=" O GLU 7 651 " (cutoff:3.500A) Processing helix chain '8' and resid 61 through 64 Processing helix chain '8' and resid 83 through 87 Processing sheet with id=1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=2, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL A 258 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.810A pdb=" N CYS A 44 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.917A pdb=" N PHE A 75 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 180 through 188 Processing sheet with id=6, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=7, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.729A pdb=" N GLN A 217 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 275 through 277 removed outlier: 7.288A pdb=" N THR A 379 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 288 through 290 removed outlier: 6.504A pdb=" N GLY A 455 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY A 315 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE A 399 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 320 through 323 Processing sheet with id=11, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.001A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=14, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.454A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.166A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.043A pdb=" N GLY L 13 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'Q' and resid 29 through 30 Processing sheet with id=17, first strand: chain 'Q' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL Q 258 " --> pdb=" O LEU Q 69 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'Q' and resid 58 through 59 removed outlier: 6.810A pdb=" N CYS Q 44 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'Q' and resid 73 through 75 removed outlier: 4.917A pdb=" N PHE Q 75 " --> pdb=" O PRO Q 253 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'Q' and resid 180 through 188 Processing sheet with id=21, first strand: chain 'Q' and resid 142 through 143 Processing sheet with id=22, first strand: chain 'Q' and resid 217 through 218 removed outlier: 6.729A pdb=" N GLN Q 217 " --> pdb=" O TYR Q 449 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'Q' and resid 275 through 277 removed outlier: 7.289A pdb=" N THR Q 379 " --> pdb=" O MET Q 482 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'Q' and resid 288 through 290 removed outlier: 6.504A pdb=" N GLY Q 455 " --> pdb=" O GLY Q 315 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY Q 315 " --> pdb=" O GLY Q 455 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE Q 399 " --> pdb=" O ARG Q 435 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 320 through 323 Processing sheet with id=26, first strand: chain 'S' and resid 4 through 5 Processing sheet with id=27, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.001A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'S' and resid 96 through 97 Processing sheet with id=29, first strand: chain 'T' and resid 4 through 7 removed outlier: 5.454A pdb=" N THR T 69 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLN T 27 " --> pdb=" O SER T 67 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N SER T 67 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE T 29 " --> pdb=" O SER T 65 " (cutoff:3.500A) removed outlier: 12.166A pdb=" N SER T 65 " --> pdb=" O ILE T 29 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'T' and resid 10 through 13 removed outlier: 4.042A pdb=" N GLY T 13 " --> pdb=" O ASP T 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain '6' and resid 29 through 30 Processing sheet with id=32, first strand: chain '6' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL 6 258 " --> pdb=" O LEU 6 69 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain '6' and resid 58 through 59 removed outlier: 6.810A pdb=" N CYS 6 44 " --> pdb=" O LEU 6 58 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain '6' and resid 73 through 75 removed outlier: 4.917A pdb=" N PHE 6 75 " --> pdb=" O PRO 6 253 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain '6' and resid 180 through 188 Processing sheet with id=36, first strand: chain '6' and resid 142 through 143 Processing sheet with id=37, first strand: chain '6' and resid 217 through 218 removed outlier: 6.728A pdb=" N GLN 6 217 " --> pdb=" O TYR 6 449 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain '6' and resid 275 through 277 removed outlier: 7.289A pdb=" N THR 6 379 " --> pdb=" O MET 6 482 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain '6' and resid 288 through 290 removed outlier: 6.504A pdb=" N GLY 6 455 " --> pdb=" O GLY 6 315 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY 6 315 " --> pdb=" O GLY 6 455 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE 6 399 " --> pdb=" O ARG 6 435 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain '6' and resid 320 through 323 Processing sheet with id=41, first strand: chain '8' and resid 4 through 5 Processing sheet with id=42, first strand: chain '8' and resid 11 through 12 removed outlier: 6.000A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain '8' and resid 96 through 97 Processing sheet with id=44, first strand: chain '9' and resid 4 through 7 removed outlier: 5.454A pdb=" N THR 9 69 " --> pdb=" O ALA 9 25 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLN 9 27 " --> pdb=" O SER 9 67 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N SER 9 67 " --> pdb=" O GLN 9 27 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE 9 29 " --> pdb=" O SER 9 65 " (cutoff:3.500A) removed outlier: 12.166A pdb=" N SER 9 65 " --> pdb=" O ILE 9 29 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain '9' and resid 10 through 13 removed outlier: 4.042A pdb=" N GLY 9 13 " --> pdb=" O ASP 9 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU 9 33 " --> pdb=" O TYR 9 49 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR 9 49 " --> pdb=" O LEU 9 33 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP 9 35 " --> pdb=" O LEU 9 47 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2007 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: 11.11 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4393 1.32 - 1.47: 8428 1.47 - 1.61: 10345 1.61 - 1.76: 41 1.76 - 1.90: 169 Bond restraints: 23376 Sorted by residual: bond pdb=" NE1 TRP Q 290 " pdb=" CE2 TRP Q 290 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.47e+01 bond pdb=" NE1 TRP A 290 " pdb=" CE2 TRP A 290 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.45e+01 bond pdb=" NE1 TRP 6 290 " pdb=" CE2 TRP 6 290 " ideal model delta sigma weight residual 1.370 1.306 0.064 1.10e-02 8.26e+03 3.41e+01 bond pdb=" CB LEU R 674 " pdb=" CG LEU R 674 " ideal model delta sigma weight residual 1.530 1.641 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" CB LEU B 674 " pdb=" CG LEU B 674 " ideal model delta sigma weight residual 1.530 1.640 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 31653 7.12 - 14.24: 108 14.24 - 21.36: 0 21.36 - 28.48: 0 28.48 - 35.60: 3 Bond angle restraints: 31764 Sorted by residual: angle pdb=" C2 NAG A 610 " pdb=" N2 NAG A 610 " pdb=" C7 NAG A 610 " ideal model delta sigma weight residual 124.56 160.16 -35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG 6 610 " pdb=" N2 NAG 6 610 " pdb=" C7 NAG 6 610 " ideal model delta sigma weight residual 124.56 160.16 -35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG Q 610 " pdb=" N2 NAG Q 610 " pdb=" C7 NAG Q 610 " ideal model delta sigma weight residual 124.56 160.14 -35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N VAL A 32 " pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 108.95 117.06 -8.11 9.80e-01 1.04e+00 6.84e+01 angle pdb=" N VAL Q 32 " pdb=" CA VAL Q 32 " pdb=" C VAL Q 32 " ideal model delta sigma weight residual 108.95 117.04 -8.09 9.80e-01 1.04e+00 6.81e+01 ... (remaining 31759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 15372 21.30 - 42.61: 447 42.61 - 63.91: 93 63.91 - 85.21: 84 85.21 - 106.51: 51 Dihedral angle restraints: 16047 sinusoidal: 8424 harmonic: 7623 Sorted by residual: dihedral pdb=" C PHE R 537 " pdb=" N PHE R 537 " pdb=" CA PHE R 537 " pdb=" CB PHE R 537 " ideal model delta harmonic sigma weight residual -122.60 -111.05 -11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE 7 537 " pdb=" N PHE 7 537 " pdb=" CA PHE 7 537 " pdb=" CB PHE 7 537 " ideal model delta harmonic sigma weight residual -122.60 -111.06 -11.54 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE B 537 " pdb=" N PHE B 537 " pdb=" CA PHE B 537 " pdb=" CB PHE B 537 " ideal model delta harmonic sigma weight residual -122.60 -111.07 -11.53 0 2.50e+00 1.60e-01 2.13e+01 ... (remaining 16044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2533 0.107 - 0.213: 858 0.213 - 0.320: 380 0.320 - 0.426: 144 0.426 - 0.533: 78 Chirality restraints: 3993 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 3990 not shown) Planarity restraints: 3885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.298 2.00e-02 2.50e+03 2.51e-01 7.86e+02 pdb=" C7 NAG A 602 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.186 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.430 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 602 " -0.298 2.00e-02 2.50e+03 2.51e-01 7.86e+02 pdb=" C7 NAG Q 602 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG Q 602 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG Q 602 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG Q 602 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 602 " -0.298 2.00e-02 2.50e+03 2.51e-01 7.85e+02 pdb=" C7 NAG 6 602 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG 6 602 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG 6 602 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG 6 602 " -0.022 2.00e-02 2.50e+03 ... (remaining 3882 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 7849 2.88 - 3.38: 20574 3.38 - 3.89: 38824 3.89 - 4.39: 45265 4.39 - 4.90: 72690 Nonbonded interactions: 185202 Sorted by model distance: nonbonded pdb=" OD1 ASP A 89 " pdb=" NZ LYS B 589 " model vdw 2.373 3.120 nonbonded pdb=" OD1 ASP Q 89 " pdb=" NZ LYS R 589 " model vdw 2.373 3.120 nonbonded pdb=" OD1 ASP 6 89 " pdb=" NZ LYS 7 589 " model vdw 2.373 3.120 nonbonded pdb=" NZ LYS A 254 " pdb=" OD2 ASP L 92 " model vdw 2.390 3.120 nonbonded pdb=" NZ LYS Q 254 " pdb=" OD2 ASP T 92 " model vdw 2.390 3.120 ... (remaining 185197 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'J' selection = chain 'g' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain 'D' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'V' selection = chain 'b' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' } ncs_group { reference = (chain '3' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } ncs_group { reference = chain '6' selection = chain 'A' selection = chain 'Q' } ncs_group { reference = chain '7' selection = chain 'B' selection = chain 'R' } ncs_group { reference = chain '8' selection = chain 'H' selection = chain 'S' } ncs_group { reference = chain '9' selection = chain 'L' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'I' selection = chain 'Z' selection = chain 'f' } 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 59.540 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.170 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.023 0.249 23580 Z= 1.217 Angle : 1.896 35.605 32343 Z= 1.182 Chirality : 0.152 0.533 3993 Planarity : 0.011 0.251 3801 Dihedral : 13.523 106.514 11013 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 1.39 % Allowed : 3.14 % Favored : 95.47 % Rotamer: Outliers : 0.39 % Allowed : 1.04 % Favored : 98.57 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2583 helix: -0.23 (0.22), residues: 429 sheet: 0.31 (0.17), residues: 720 loop : -0.32 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.008 TRP A 290 HIS 0.008 0.002 HIS S 100N PHE 0.049 0.008 PHE R 537 TYR 0.057 0.009 TYR H 91 ARG 0.011 0.001 ARG 6 231 Details of bonding type rmsd link_TRANS : bond 0.00559 ( 9) link_TRANS : angle 1.58406 ( 27) link_NAG-ASN : bond 0.07841 ( 75) link_NAG-ASN : angle 2.82176 ( 225) link_ALPHA1-6 : bond 0.05477 ( 12) link_ALPHA1-6 : angle 3.74196 ( 36) link_BETA1-4 : bond 0.07212 ( 48) link_BETA1-4 : angle 4.44336 ( 144) link_ALPHA1-2 : bond 0.08532 ( 6) link_ALPHA1-2 : angle 4.13134 ( 18) link_ALPHA1-3 : bond 0.08691 ( 12) link_ALPHA1-3 : angle 4.47246 ( 36) hydrogen bonds : bond 0.18789 ( 780) hydrogen bonds : angle 7.59337 ( 2007) link_BETA1-6 : bond 0.05504 ( 9) link_BETA1-6 : angle 2.93748 ( 27) SS BOND : bond 0.07562 ( 33) SS BOND : angle 2.85578 ( 66) covalent geometry : bond 0.02258 (23376) covalent geometry : angle 1.85451 (31764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 511 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7089 (t0) REVERT: A 338 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7347 (mmt180) REVERT: B 553 THR cc_start: 0.6849 (p) cc_final: 0.6330 (t) REVERT: B 590 ASN cc_start: 0.5725 (m-40) cc_final: 0.5139 (t0) REVERT: H 21 THR cc_start: 0.8477 (m) cc_final: 0.7922 (p) REVERT: H 32 CYS cc_start: 0.7015 (t) cc_final: 0.6748 (p) REVERT: H 82 ASN cc_start: 0.6998 (p0) cc_final: 0.6641 (p0) REVERT: Q 172 MET cc_start: 0.8144 (tpp) cc_final: 0.7897 (tpt) REVERT: Q 205 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7946 (mtm-85) REVERT: Q 306 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6917 (t0) REVERT: Q 338 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7168 (mmp80) REVERT: Q 473 ILE cc_start: 0.8710 (pt) cc_final: 0.8261 (mt) REVERT: R 553 THR cc_start: 0.6820 (p) cc_final: 0.6595 (t) REVERT: R 590 ASN cc_start: 0.5176 (m-40) cc_final: 0.4625 (t0) REVERT: R 625 TRP cc_start: 0.7375 (t-100) cc_final: 0.7129 (t-100) REVERT: R 668 MET cc_start: 0.6390 (tpp) cc_final: 0.5536 (mmp) REVERT: S 21 THR cc_start: 0.8219 (m) cc_final: 0.7835 (p) REVERT: S 32 CYS cc_start: 0.6893 (t) cc_final: 0.6650 (p) REVERT: S 69 ILE cc_start: 0.7347 (mt) cc_final: 0.7030 (mt) REVERT: S 73 MET cc_start: 0.7020 (mtt) cc_final: 0.6715 (mmm) REVERT: 6 306 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6818 (t0) REVERT: 6 338 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7291 (mmt-90) REVERT: 7 553 THR cc_start: 0.6745 (p) cc_final: 0.6467 (t) REVERT: 7 590 ASN cc_start: 0.5115 (m-40) cc_final: 0.4508 (t0) REVERT: 7 611 TRP cc_start: 0.7438 (m-10) cc_final: 0.7212 (m-10) REVERT: 7 625 TRP cc_start: 0.7239 (t-100) cc_final: 0.6964 (t-100) REVERT: 7 667 ASN cc_start: 0.7015 (m-40) cc_final: 0.6581 (t0) outliers start: 9 outliers final: 0 residues processed: 515 average time/residue: 0.3882 time to fit residues: 297.7431 Evaluate side-chains 271 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 265 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 338 ARG Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 338 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 223 HIS ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 56 ASN H 77 GLN Q 223 HIS ** R 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 223 HIS ** 7 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106373 restraints weight = 30203.575| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.87 r_work: 0.3177 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23580 Z= 0.200 Angle : 0.859 12.292 32343 Z= 0.424 Chirality : 0.051 0.396 3993 Planarity : 0.005 0.052 3801 Dihedral : 11.310 84.745 6126 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.56 % Favored : 95.86 % Rotamer: Outliers : 1.73 % Allowed : 7.45 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2583 helix: 1.21 (0.24), residues: 438 sheet: 0.25 (0.17), residues: 750 loop : -0.69 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 6 91 HIS 0.005 0.001 HIS Q 210 PHE 0.025 0.003 PHE R 537 TYR 0.020 0.002 TYR A 401 ARG 0.009 0.001 ARG 8 38 Details of bonding type rmsd link_TRANS : bond 0.00110 ( 9) link_TRANS : angle 0.71104 ( 27) link_NAG-ASN : bond 0.00602 ( 75) link_NAG-ASN : angle 2.88727 ( 225) link_ALPHA1-6 : bond 0.00583 ( 12) link_ALPHA1-6 : angle 1.66691 ( 36) link_BETA1-4 : bond 0.00705 ( 48) link_BETA1-4 : angle 2.51992 ( 144) link_ALPHA1-2 : bond 0.00127 ( 6) link_ALPHA1-2 : angle 2.13462 ( 18) link_ALPHA1-3 : bond 0.01101 ( 12) link_ALPHA1-3 : angle 1.66865 ( 36) hydrogen bonds : bond 0.06441 ( 780) hydrogen bonds : angle 6.15842 ( 2007) link_BETA1-6 : bond 0.00897 ( 9) link_BETA1-6 : angle 1.05739 ( 27) SS BOND : bond 0.00313 ( 33) SS BOND : angle 0.83749 ( 66) covalent geometry : bond 0.00442 (23376) covalent geometry : angle 0.80746 (31764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.7669 (mttt) cc_final: 0.7449 (mtpt) REVERT: A 290 TRP cc_start: 0.8340 (m100) cc_final: 0.7753 (m100) REVERT: B 553 THR cc_start: 0.6358 (p) cc_final: 0.5850 (t) REVERT: B 590 ASN cc_start: 0.5310 (m-40) cc_final: 0.5105 (m-40) REVERT: B 641 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7303 (mp0) REVERT: B 668 MET cc_start: 0.6321 (tpt) cc_final: 0.5998 (tpp) REVERT: H 6 GLU cc_start: 0.5872 (mp0) cc_final: 0.5543 (mp0) REVERT: H 21 THR cc_start: 0.7752 (m) cc_final: 0.7494 (p) REVERT: H 55 ASP cc_start: 0.8091 (m-30) cc_final: 0.7813 (m-30) REVERT: L 39 LYS cc_start: 0.7476 (mmmt) cc_final: 0.7099 (mmtm) REVERT: L 91 TYR cc_start: 0.8152 (p90) cc_final: 0.7694 (p90) REVERT: Q 172 MET cc_start: 0.8354 (tpp) cc_final: 0.8145 (tpt) REVERT: Q 193 VAL cc_start: 0.8707 (t) cc_final: 0.8490 (m) REVERT: R 553 THR cc_start: 0.6423 (p) cc_final: 0.5050 (t) REVERT: R 557 ARG cc_start: 0.6264 (mtm110) cc_final: 0.5945 (ttp80) REVERT: R 599 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: R 631 ILE cc_start: 0.8231 (tp) cc_final: 0.7939 (mt) REVERT: R 641 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7341 (mp0) REVERT: S 5 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8134 (tp-100) REVERT: 6 95 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7650 (tp30) REVERT: 6 103 LYS cc_start: 0.8788 (mttt) cc_final: 0.8524 (mttt) REVERT: 6 120 ARG cc_start: 0.8674 (ttp-170) cc_final: 0.8447 (ttm170) REVERT: 6 257 LYS cc_start: 0.8084 (mttt) cc_final: 0.7699 (mtpt) REVERT: 6 281 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8201 (mtp-110) REVERT: 6 325 MET cc_start: 0.8440 (mtm) cc_final: 0.8085 (mtp) REVERT: 7 545 MET cc_start: 0.7095 (mtp) cc_final: 0.6795 (mtp) REVERT: 7 553 THR cc_start: 0.6769 (p) cc_final: 0.6276 (t) REVERT: 7 625 TRP cc_start: 0.7311 (t-100) cc_final: 0.6672 (t-100) REVERT: 7 667 ASN cc_start: 0.7003 (m-40) cc_final: 0.6607 (t0) REVERT: 7 668 MET cc_start: 0.6271 (tpt) cc_final: 0.5556 (tpp) REVERT: 8 6 GLU cc_start: 0.5676 (mp0) cc_final: 0.5423 (mp0) REVERT: 8 21 THR cc_start: 0.7818 (m) cc_final: 0.7409 (p) REVERT: 8 53 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7906 (t70) outliers start: 40 outliers final: 28 residues processed: 369 average time/residue: 0.3531 time to fit residues: 201.1697 Evaluate side-chains 308 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 203 GLU Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 53 ASP Chi-restraints excluded: chain 8 residue 87 THR Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 9 residue 33 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 114 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110629 restraints weight = 30769.309| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.70 r_work: 0.3098 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 23580 Z= 0.163 Angle : 0.723 13.998 32343 Z= 0.356 Chirality : 0.046 0.324 3993 Planarity : 0.004 0.041 3801 Dihedral : 9.684 75.900 6114 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.57 % Favored : 94.97 % Rotamer: Outliers : 1.90 % Allowed : 9.44 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2583 helix: 1.18 (0.24), residues: 453 sheet: 0.16 (0.19), residues: 705 loop : -0.95 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 6 91 HIS 0.002 0.001 HIS Q 364 PHE 0.021 0.002 PHE 7 537 TYR 0.022 0.001 TYR 6 401 ARG 0.010 0.001 ARG R 594 Details of bonding type rmsd link_TRANS : bond 0.00095 ( 9) link_TRANS : angle 0.52446 ( 27) link_NAG-ASN : bond 0.00466 ( 75) link_NAG-ASN : angle 2.38097 ( 225) link_ALPHA1-6 : bond 0.00821 ( 12) link_ALPHA1-6 : angle 1.67685 ( 36) link_BETA1-4 : bond 0.00656 ( 48) link_BETA1-4 : angle 1.87798 ( 144) link_ALPHA1-2 : bond 0.00365 ( 6) link_ALPHA1-2 : angle 1.68839 ( 18) link_ALPHA1-3 : bond 0.01297 ( 12) link_ALPHA1-3 : angle 1.48203 ( 36) hydrogen bonds : bond 0.05080 ( 780) hydrogen bonds : angle 5.69977 ( 2007) link_BETA1-6 : bond 0.00716 ( 9) link_BETA1-6 : angle 1.10001 ( 27) SS BOND : bond 0.00249 ( 33) SS BOND : angle 0.71739 ( 66) covalent geometry : bond 0.00351 (23376) covalent geometry : angle 0.68304 (31764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8048 (tt) REVERT: A 257 LYS cc_start: 0.7644 (mttt) cc_final: 0.7408 (mtpt) REVERT: A 290 TRP cc_start: 0.8252 (m100) cc_final: 0.7853 (m100) REVERT: A 309 MET cc_start: 0.8382 (ttp) cc_final: 0.8146 (ttt) REVERT: B 553 THR cc_start: 0.5991 (p) cc_final: 0.5581 (t) REVERT: B 590 ASN cc_start: 0.5069 (m-40) cc_final: 0.4664 (t0) REVERT: B 641 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7172 (mp0) REVERT: B 668 MET cc_start: 0.6116 (tpt) cc_final: 0.5626 (tpp) REVERT: H 6 GLU cc_start: 0.5978 (mp0) cc_final: 0.5738 (mp0) REVERT: H 55 ASP cc_start: 0.8180 (m-30) cc_final: 0.7939 (m-30) REVERT: L 91 TYR cc_start: 0.8086 (p90) cc_final: 0.7649 (p90) REVERT: Q 88 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6903 (tm-30) REVERT: Q 172 MET cc_start: 0.8431 (tpp) cc_final: 0.8204 (tpt) REVERT: Q 309 MET cc_start: 0.8565 (ttt) cc_final: 0.8209 (ttt) REVERT: R 599 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: R 631 ILE cc_start: 0.8229 (tp) cc_final: 0.7991 (mt) REVERT: S 13 ARG cc_start: 0.8276 (mpt180) cc_final: 0.8051 (tpp80) REVERT: S 46 GLU cc_start: 0.7825 (tt0) cc_final: 0.7401 (pt0) REVERT: S 55 ASP cc_start: 0.8162 (m-30) cc_final: 0.7839 (m-30) REVERT: T 33 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8531 (tp) REVERT: 6 257 LYS cc_start: 0.8014 (mttt) cc_final: 0.7657 (mtpt) REVERT: 6 309 MET cc_start: 0.8447 (ttt) cc_final: 0.8179 (ttt) REVERT: 6 325 MET cc_start: 0.8328 (mtm) cc_final: 0.8027 (mtp) REVERT: 7 545 MET cc_start: 0.7095 (mtp) cc_final: 0.6864 (mtp) REVERT: 7 553 THR cc_start: 0.6373 (p) cc_final: 0.5767 (t) REVERT: 7 557 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.6168 (ttm110) REVERT: 7 667 ASN cc_start: 0.6988 (m-40) cc_final: 0.6605 (t0) REVERT: 7 668 MET cc_start: 0.6255 (tpt) cc_final: 0.5420 (tpp) REVERT: 8 77 GLN cc_start: 0.7874 (mt0) cc_final: 0.7660 (mm-40) REVERT: 8 105 GLN cc_start: 0.8606 (mm110) cc_final: 0.8178 (tm-30) outliers start: 44 outliers final: 29 residues processed: 313 average time/residue: 0.4946 time to fit residues: 235.6386 Evaluate side-chains 274 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 557 ARG Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 9 residue 3 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 640 GLN S 82AASN S 105 GLN 7 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.150783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111116 restraints weight = 31114.299| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.72 r_work: 0.3106 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23580 Z= 0.139 Angle : 0.676 9.099 32343 Z= 0.331 Chirality : 0.045 0.321 3993 Planarity : 0.004 0.049 3801 Dihedral : 8.834 69.166 6112 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.41 % Favored : 95.16 % Rotamer: Outliers : 2.08 % Allowed : 10.04 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2583 helix: 1.52 (0.24), residues: 453 sheet: 0.11 (0.18), residues: 738 loop : -0.98 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 625 HIS 0.002 0.001 HIS A 364 PHE 0.016 0.002 PHE 7 537 TYR 0.030 0.001 TYR 9 91 ARG 0.009 0.000 ARG 7 594 Details of bonding type rmsd link_TRANS : bond 0.00090 ( 9) link_TRANS : angle 0.42381 ( 27) link_NAG-ASN : bond 0.00400 ( 75) link_NAG-ASN : angle 2.28920 ( 225) link_ALPHA1-6 : bond 0.00892 ( 12) link_ALPHA1-6 : angle 1.86905 ( 36) link_BETA1-4 : bond 0.00541 ( 48) link_BETA1-4 : angle 1.68871 ( 144) link_ALPHA1-2 : bond 0.00274 ( 6) link_ALPHA1-2 : angle 1.65743 ( 18) link_ALPHA1-3 : bond 0.01175 ( 12) link_ALPHA1-3 : angle 1.67216 ( 36) hydrogen bonds : bond 0.04478 ( 780) hydrogen bonds : angle 5.47248 ( 2007) link_BETA1-6 : bond 0.00710 ( 9) link_BETA1-6 : angle 1.06630 ( 27) SS BOND : bond 0.00453 ( 33) SS BOND : angle 0.95608 ( 66) covalent geometry : bond 0.00307 (23376) covalent geometry : angle 0.63532 (31764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 TRP cc_start: 0.8241 (m100) cc_final: 0.7989 (m100) REVERT: A 309 MET cc_start: 0.8287 (ttp) cc_final: 0.8055 (ttt) REVERT: A 501 GLU cc_start: 0.7942 (tt0) cc_final: 0.7691 (tt0) REVERT: B 553 THR cc_start: 0.5644 (p) cc_final: 0.5415 (t) REVERT: B 590 ASN cc_start: 0.4723 (m-40) cc_final: 0.4473 (t0) REVERT: B 625 TRP cc_start: 0.6819 (t-100) cc_final: 0.6463 (t-100) REVERT: B 668 MET cc_start: 0.6160 (tpt) cc_final: 0.5626 (tpt) REVERT: H 6 GLU cc_start: 0.6009 (mp0) cc_final: 0.5709 (mp0) REVERT: H 55 ASP cc_start: 0.8234 (m-30) cc_final: 0.8023 (m-30) REVERT: H 77 GLN cc_start: 0.7796 (mt0) cc_final: 0.7475 (mm110) REVERT: L 91 TYR cc_start: 0.8074 (p90) cc_final: 0.7626 (p90) REVERT: Q 88 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6953 (tm-30) REVERT: Q 172 MET cc_start: 0.8506 (tpp) cc_final: 0.8298 (tpt) REVERT: Q 290 TRP cc_start: 0.8319 (m100) cc_final: 0.8017 (m100) REVERT: Q 309 MET cc_start: 0.8430 (ttt) cc_final: 0.8227 (ttt) REVERT: R 599 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: R 668 MET cc_start: 0.5619 (tpt) cc_final: 0.5051 (tpp) REVERT: S 46 GLU cc_start: 0.7844 (tt0) cc_final: 0.7471 (pt0) REVERT: S 55 ASP cc_start: 0.8227 (m-30) cc_final: 0.7900 (m-30) REVERT: S 56 ASN cc_start: 0.8698 (m110) cc_final: 0.8488 (m-40) REVERT: T 33 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8474 (tp) REVERT: 6 95 GLU cc_start: 0.7689 (tp30) cc_final: 0.7082 (tp30) REVERT: 6 257 LYS cc_start: 0.8046 (mttt) cc_final: 0.7710 (mtpt) REVERT: 6 309 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (ttt) REVERT: 7 545 MET cc_start: 0.7259 (mtp) cc_final: 0.6886 (mtp) REVERT: 7 667 ASN cc_start: 0.6993 (m-40) cc_final: 0.6592 (t0) REVERT: 7 668 MET cc_start: 0.6172 (tpt) cc_final: 0.5647 (tpp) REVERT: 8 32 CYS cc_start: 0.7031 (p) cc_final: 0.6722 (m) REVERT: 8 77 GLN cc_start: 0.7892 (mt0) cc_final: 0.7430 (mm110) REVERT: 8 105 GLN cc_start: 0.8542 (mm110) cc_final: 0.8196 (tm-30) REVERT: 9 42 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8436 (pttm) outliers start: 48 outliers final: 35 residues processed: 299 average time/residue: 0.4514 time to fit residues: 212.0038 Evaluate side-chains 260 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 309 MET Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 11 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100NHIS S 82AASN 7 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.182733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.146231 restraints weight = 31847.154| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.37 r_work: 0.3575 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23580 Z= 0.171 Angle : 0.679 8.161 32343 Z= 0.334 Chirality : 0.046 0.317 3993 Planarity : 0.004 0.045 3801 Dihedral : 8.498 66.309 6112 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.11 % Favored : 94.39 % Rotamer: Outliers : 2.38 % Allowed : 10.43 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2583 helix: 1.61 (0.24), residues: 456 sheet: 0.05 (0.19), residues: 708 loop : -1.14 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 625 HIS 0.003 0.001 HIS Q 364 PHE 0.017 0.002 PHE 7 537 TYR 0.023 0.002 TYR 6 401 ARG 0.007 0.001 ARG R 594 Details of bonding type rmsd link_TRANS : bond 0.00123 ( 9) link_TRANS : angle 0.41411 ( 27) link_NAG-ASN : bond 0.00367 ( 75) link_NAG-ASN : angle 2.19593 ( 225) link_ALPHA1-6 : bond 0.00836 ( 12) link_ALPHA1-6 : angle 1.83839 ( 36) link_BETA1-4 : bond 0.00509 ( 48) link_BETA1-4 : angle 1.56718 ( 144) link_ALPHA1-2 : bond 0.00291 ( 6) link_ALPHA1-2 : angle 1.59891 ( 18) link_ALPHA1-3 : bond 0.01162 ( 12) link_ALPHA1-3 : angle 1.69089 ( 36) hydrogen bonds : bond 0.04406 ( 780) hydrogen bonds : angle 5.41981 ( 2007) link_BETA1-6 : bond 0.00607 ( 9) link_BETA1-6 : angle 1.10816 ( 27) SS BOND : bond 0.00363 ( 33) SS BOND : angle 1.56212 ( 66) covalent geometry : bond 0.00399 (23376) covalent geometry : angle 0.64017 (31764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 553 THR cc_start: 0.5765 (p) cc_final: 0.5548 (t) REVERT: B 590 ASN cc_start: 0.4754 (m-40) cc_final: 0.4473 (t0) REVERT: B 668 MET cc_start: 0.6233 (tpt) cc_final: 0.5950 (tpt) REVERT: H 6 GLU cc_start: 0.6114 (mp0) cc_final: 0.5777 (mp0) REVERT: H 32 CYS cc_start: 0.7152 (p) cc_final: 0.6845 (m) REVERT: H 55 ASP cc_start: 0.8262 (m-30) cc_final: 0.8004 (m-30) REVERT: H 72 ASP cc_start: 0.7407 (t0) cc_final: 0.7133 (t0) REVERT: L 91 TYR cc_start: 0.8172 (p90) cc_final: 0.7967 (p90) REVERT: Q 88 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7449 (tm-30) REVERT: Q 91 TRP cc_start: 0.7254 (t-100) cc_final: 0.6914 (t-100) REVERT: Q 172 MET cc_start: 0.8424 (tpp) cc_final: 0.8168 (tpt) REVERT: Q 290 TRP cc_start: 0.8426 (m100) cc_final: 0.8218 (m100) REVERT: R 609 ASN cc_start: 0.7576 (m-40) cc_final: 0.7349 (m-40) REVERT: R 668 MET cc_start: 0.5644 (tpt) cc_final: 0.5071 (tpp) REVERT: S 32 CYS cc_start: 0.6972 (p) cc_final: 0.6712 (m) REVERT: S 46 GLU cc_start: 0.7817 (tt0) cc_final: 0.7566 (pt0) REVERT: S 55 ASP cc_start: 0.8110 (m-30) cc_final: 0.7870 (m-30) REVERT: T 33 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8478 (tp) REVERT: 6 91 TRP cc_start: 0.7180 (t-100) cc_final: 0.6706 (t-100) REVERT: 6 95 GLU cc_start: 0.8068 (tp30) cc_final: 0.7527 (tp30) REVERT: 6 257 LYS cc_start: 0.8443 (mttt) cc_final: 0.8218 (mtpt) REVERT: 7 545 MET cc_start: 0.7450 (mtp) cc_final: 0.7037 (mtp) REVERT: 7 667 ASN cc_start: 0.6900 (m-40) cc_final: 0.6462 (t0) REVERT: 7 668 MET cc_start: 0.6355 (tpt) cc_final: 0.5811 (tpp) outliers start: 55 outliers final: 46 residues processed: 297 average time/residue: 0.3389 time to fit residues: 157.7990 Evaluate side-chains 273 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 73 optimal weight: 4.9990 chunk 125 optimal weight: 0.0370 chunk 251 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 142 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN H 77 GLN S 82AASN S 100NHIS T 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.183870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147817 restraints weight = 31538.624| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.33 r_work: 0.3607 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23580 Z= 0.140 Angle : 0.650 8.876 32343 Z= 0.320 Chirality : 0.045 0.303 3993 Planarity : 0.004 0.050 3801 Dihedral : 8.212 61.910 6112 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.23 % Favored : 94.23 % Rotamer: Outliers : 2.21 % Allowed : 11.26 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2583 helix: 1.84 (0.24), residues: 453 sheet: 0.02 (0.19), residues: 693 loop : -1.19 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 6 91 HIS 0.002 0.001 HIS 6 364 PHE 0.015 0.002 PHE 7 537 TYR 0.017 0.001 TYR 9 91 ARG 0.011 0.001 ARG 6 313 Details of bonding type rmsd link_TRANS : bond 0.00083 ( 9) link_TRANS : angle 0.41516 ( 27) link_NAG-ASN : bond 0.00358 ( 75) link_NAG-ASN : angle 2.07102 ( 225) link_ALPHA1-6 : bond 0.00889 ( 12) link_ALPHA1-6 : angle 1.85725 ( 36) link_BETA1-4 : bond 0.00508 ( 48) link_BETA1-4 : angle 1.42140 ( 144) link_ALPHA1-2 : bond 0.00298 ( 6) link_ALPHA1-2 : angle 1.55739 ( 18) link_ALPHA1-3 : bond 0.01201 ( 12) link_ALPHA1-3 : angle 1.71325 ( 36) hydrogen bonds : bond 0.04113 ( 780) hydrogen bonds : angle 5.30086 ( 2007) link_BETA1-6 : bond 0.00638 ( 9) link_BETA1-6 : angle 1.10532 ( 27) SS BOND : bond 0.00366 ( 33) SS BOND : angle 1.56109 ( 66) covalent geometry : bond 0.00319 (23376) covalent geometry : angle 0.61290 (31764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8600 (tp40) cc_final: 0.8121 (tp40) REVERT: B 553 THR cc_start: 0.5875 (p) cc_final: 0.5663 (t) REVERT: B 590 ASN cc_start: 0.4806 (m-40) cc_final: 0.4544 (t0) REVERT: B 609 ASN cc_start: 0.7336 (m-40) cc_final: 0.7063 (m-40) REVERT: B 668 MET cc_start: 0.6147 (tpt) cc_final: 0.5862 (tpt) REVERT: H 6 GLU cc_start: 0.6464 (mp0) cc_final: 0.6196 (mp0) REVERT: H 32 CYS cc_start: 0.7086 (p) cc_final: 0.6764 (m) REVERT: H 55 ASP cc_start: 0.8224 (m-30) cc_final: 0.7989 (m-30) REVERT: H 81 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7618 (ttmm) REVERT: Q 88 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7454 (tm-30) REVERT: Q 91 TRP cc_start: 0.7214 (t-100) cc_final: 0.6965 (t-100) REVERT: Q 172 MET cc_start: 0.8380 (tpp) cc_final: 0.8143 (tpt) REVERT: Q 203 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6799 (pp20) REVERT: Q 221 ASP cc_start: 0.7567 (t0) cc_final: 0.7245 (t70) REVERT: R 609 ASN cc_start: 0.7532 (m-40) cc_final: 0.7324 (m-40) REVERT: R 668 MET cc_start: 0.5622 (tpt) cc_final: 0.5071 (tpp) REVERT: S 32 CYS cc_start: 0.7044 (p) cc_final: 0.6780 (m) REVERT: S 55 ASP cc_start: 0.8079 (m-30) cc_final: 0.7826 (m-30) REVERT: T 33 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8416 (tp) REVERT: 6 91 TRP cc_start: 0.7100 (t-100) cc_final: 0.6679 (t-100) REVERT: 6 95 GLU cc_start: 0.7971 (tp30) cc_final: 0.7494 (tp30) REVERT: 6 221 ASP cc_start: 0.7809 (t0) cc_final: 0.7475 (t70) REVERT: 7 668 MET cc_start: 0.6351 (tpt) cc_final: 0.5721 (tpp) outliers start: 51 outliers final: 42 residues processed: 287 average time/residue: 0.3512 time to fit residues: 158.6124 Evaluate side-chains 270 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 203 GLU Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 306 ASN Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 28 THR Chi-restraints excluded: chain 8 residue 46 GLU Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 14 optimal weight: 0.5980 chunk 237 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN S 56 ASN S 82AASN S 105 GLN 9 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.180514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144073 restraints weight = 31912.013| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.36 r_work: 0.3544 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23580 Z= 0.179 Angle : 0.676 10.807 32343 Z= 0.332 Chirality : 0.045 0.311 3993 Planarity : 0.004 0.043 3801 Dihedral : 8.132 60.203 6110 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.04 % Favored : 93.46 % Rotamer: Outliers : 2.64 % Allowed : 11.65 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2583 helix: 1.92 (0.24), residues: 453 sheet: -0.09 (0.19), residues: 708 loop : -1.33 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 345 HIS 0.004 0.001 HIS 6 364 PHE 0.017 0.002 PHE H 78 TYR 0.025 0.002 TYR 6 401 ARG 0.009 0.001 ARG 7 594 Details of bonding type rmsd link_TRANS : bond 0.00133 ( 9) link_TRANS : angle 0.40192 ( 27) link_NAG-ASN : bond 0.00342 ( 75) link_NAG-ASN : angle 2.07960 ( 225) link_ALPHA1-6 : bond 0.00823 ( 12) link_ALPHA1-6 : angle 1.81881 ( 36) link_BETA1-4 : bond 0.00486 ( 48) link_BETA1-4 : angle 1.41829 ( 144) link_ALPHA1-2 : bond 0.00364 ( 6) link_ALPHA1-2 : angle 1.60076 ( 18) link_ALPHA1-3 : bond 0.01103 ( 12) link_ALPHA1-3 : angle 1.76267 ( 36) hydrogen bonds : bond 0.04201 ( 780) hydrogen bonds : angle 5.32219 ( 2007) link_BETA1-6 : bond 0.00559 ( 9) link_BETA1-6 : angle 1.12945 ( 27) SS BOND : bond 0.00529 ( 33) SS BOND : angle 1.46693 ( 66) covalent geometry : bond 0.00423 (23376) covalent geometry : angle 0.64102 (31764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 92 GLN cc_start: 0.8629 (tp40) cc_final: 0.8041 (tp40) REVERT: B 553 THR cc_start: 0.5985 (p) cc_final: 0.5600 (t) REVERT: B 590 ASN cc_start: 0.4852 (m-40) cc_final: 0.4636 (t0) REVERT: B 609 ASN cc_start: 0.7312 (m-40) cc_final: 0.7038 (m-40) REVERT: B 633 LYS cc_start: 0.7500 (mmtm) cc_final: 0.7225 (mmtm) REVERT: B 668 MET cc_start: 0.6427 (tpt) cc_final: 0.6164 (tpt) REVERT: H 6 GLU cc_start: 0.6306 (mp0) cc_final: 0.6061 (mp0) REVERT: H 32 CYS cc_start: 0.7030 (p) cc_final: 0.6738 (m) REVERT: H 55 ASP cc_start: 0.8267 (m-30) cc_final: 0.8056 (m-30) REVERT: H 94 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7339 (mtm-85) REVERT: Q 88 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7510 (tm-30) REVERT: Q 172 MET cc_start: 0.8452 (tpp) cc_final: 0.8201 (tpt) REVERT: Q 186 THR cc_start: 0.9109 (m) cc_final: 0.8678 (p) REVERT: Q 221 ASP cc_start: 0.7846 (t0) cc_final: 0.7510 (t70) REVERT: R 668 MET cc_start: 0.5748 (tpt) cc_final: 0.5229 (tpp) REVERT: S 32 CYS cc_start: 0.7156 (p) cc_final: 0.6913 (m) REVERT: T 33 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8509 (tp) REVERT: T 39 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7619 (mmtm) REVERT: T 69 THR cc_start: 0.8081 (p) cc_final: 0.7830 (p) REVERT: 6 91 TRP cc_start: 0.7266 (t-100) cc_final: 0.6754 (t-100) REVERT: 6 95 GLU cc_start: 0.8087 (tp30) cc_final: 0.7563 (tp30) REVERT: 6 221 ASP cc_start: 0.7552 (t0) cc_final: 0.7283 (t70) REVERT: 7 668 MET cc_start: 0.6444 (tpt) cc_final: 0.5815 (tpp) outliers start: 61 outliers final: 45 residues processed: 298 average time/residue: 0.3394 time to fit residues: 160.1980 Evaluate side-chains 283 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 203 GLU Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 388 VAL Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 100 ASN Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 68 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 214 optimal weight: 0.2980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN L 79 GLN S 82AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.182336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.146474 restraints weight = 31760.600| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 3.10 r_work: 0.3580 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 23580 Z= 0.139 Angle : 0.640 10.443 32343 Z= 0.314 Chirality : 0.044 0.296 3993 Planarity : 0.004 0.051 3801 Dihedral : 7.897 59.973 6108 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.65 % Favored : 93.81 % Rotamer: Outliers : 2.25 % Allowed : 12.38 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2583 helix: 1.97 (0.24), residues: 453 sheet: -0.09 (0.19), residues: 693 loop : -1.30 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 6 345 HIS 0.002 0.001 HIS 6 364 PHE 0.015 0.002 PHE 7 537 TYR 0.017 0.001 TYR A 401 ARG 0.008 0.000 ARG B 594 Details of bonding type rmsd link_TRANS : bond 0.00085 ( 9) link_TRANS : angle 0.42767 ( 27) link_NAG-ASN : bond 0.00332 ( 75) link_NAG-ASN : angle 1.96870 ( 225) link_ALPHA1-6 : bond 0.00872 ( 12) link_ALPHA1-6 : angle 1.81534 ( 36) link_BETA1-4 : bond 0.00490 ( 48) link_BETA1-4 : angle 1.33232 ( 144) link_ALPHA1-2 : bond 0.00339 ( 6) link_ALPHA1-2 : angle 1.53349 ( 18) link_ALPHA1-3 : bond 0.01183 ( 12) link_ALPHA1-3 : angle 1.74204 ( 36) hydrogen bonds : bond 0.03982 ( 780) hydrogen bonds : angle 5.24296 ( 2007) link_BETA1-6 : bond 0.00600 ( 9) link_BETA1-6 : angle 1.12131 ( 27) SS BOND : bond 0.00437 ( 33) SS BOND : angle 0.98670 ( 66) covalent geometry : bond 0.00318 (23376) covalent geometry : angle 0.60791 (31764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8510 (tp40) cc_final: 0.8264 (mm-40) REVERT: B 553 THR cc_start: 0.5835 (p) cc_final: 0.5631 (t) REVERT: B 590 ASN cc_start: 0.5014 (m-40) cc_final: 0.4765 (t0) REVERT: B 609 ASN cc_start: 0.7342 (m-40) cc_final: 0.7091 (m-40) REVERT: B 668 MET cc_start: 0.6274 (tpt) cc_final: 0.5659 (tpp) REVERT: H 6 GLU cc_start: 0.6265 (mp0) cc_final: 0.6027 (mp0) REVERT: H 32 CYS cc_start: 0.7013 (p) cc_final: 0.6764 (m) REVERT: Q 172 MET cc_start: 0.8414 (tpp) cc_final: 0.8168 (tpt) REVERT: Q 186 THR cc_start: 0.9137 (m) cc_final: 0.8836 (p) REVERT: Q 221 ASP cc_start: 0.7768 (t0) cc_final: 0.7366 (t70) REVERT: R 571 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.4584 (mt) REVERT: R 594 ARG cc_start: 0.6912 (ttp80) cc_final: 0.6630 (tmm160) REVERT: R 668 MET cc_start: 0.5677 (tpt) cc_final: 0.5174 (tpp) REVERT: T 33 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8415 (tp) REVERT: T 69 THR cc_start: 0.8097 (p) cc_final: 0.7835 (p) REVERT: 6 91 TRP cc_start: 0.7185 (t-100) cc_final: 0.6724 (t-100) REVERT: 6 95 GLU cc_start: 0.8141 (tp30) cc_final: 0.7676 (tp30) REVERT: 6 221 ASP cc_start: 0.7352 (t0) cc_final: 0.7018 (t70) REVERT: 7 667 ASN cc_start: 0.6900 (m-40) cc_final: 0.6497 (t0) REVERT: 7 668 MET cc_start: 0.6281 (tpt) cc_final: 0.5758 (tpp) REVERT: 8 64 LYS cc_start: 0.8455 (mmmm) cc_final: 0.8194 (mmmt) REVERT: 8 77 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7051 (mm-40) outliers start: 52 outliers final: 42 residues processed: 286 average time/residue: 0.3342 time to fit residues: 151.8257 Evaluate side-chains 276 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 571 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 28 THR Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 226 optimal weight: 9.9990 chunk 200 optimal weight: 0.5980 chunk 256 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 248 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 672 GLN H 77 GLN S 82AASN S 105 GLN T 30 ASN 8 100NHIS 9 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.183446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147333 restraints weight = 31957.612| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.15 r_work: 0.3592 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23580 Z= 0.128 Angle : 0.624 8.252 32343 Z= 0.306 Chirality : 0.044 0.291 3993 Planarity : 0.004 0.051 3801 Dihedral : 7.632 59.866 6108 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.81 % Favored : 93.65 % Rotamer: Outliers : 2.03 % Allowed : 12.94 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2583 helix: 2.27 (0.24), residues: 435 sheet: -0.09 (0.19), residues: 729 loop : -1.36 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 6 345 HIS 0.002 0.000 HIS 6 364 PHE 0.029 0.002 PHE 6 346 TYR 0.016 0.001 TYR A 401 ARG 0.008 0.000 ARG B 594 Details of bonding type rmsd link_TRANS : bond 0.00076 ( 9) link_TRANS : angle 0.39955 ( 27) link_NAG-ASN : bond 0.00330 ( 75) link_NAG-ASN : angle 1.97468 ( 225) link_ALPHA1-6 : bond 0.00867 ( 12) link_ALPHA1-6 : angle 1.75130 ( 36) link_BETA1-4 : bond 0.00508 ( 48) link_BETA1-4 : angle 1.29473 ( 144) link_ALPHA1-2 : bond 0.00380 ( 6) link_ALPHA1-2 : angle 1.50943 ( 18) link_ALPHA1-3 : bond 0.01183 ( 12) link_ALPHA1-3 : angle 1.73881 ( 36) hydrogen bonds : bond 0.03825 ( 780) hydrogen bonds : angle 5.13617 ( 2007) link_BETA1-6 : bond 0.00643 ( 9) link_BETA1-6 : angle 1.11719 ( 27) SS BOND : bond 0.00461 ( 33) SS BOND : angle 0.87067 ( 66) covalent geometry : bond 0.00289 (23376) covalent geometry : angle 0.59176 (31764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8494 (tp40) cc_final: 0.8268 (mm-40) REVERT: B 590 ASN cc_start: 0.4912 (m-40) cc_final: 0.4681 (t0) REVERT: B 609 ASN cc_start: 0.7266 (m-40) cc_final: 0.7008 (m-40) REVERT: B 668 MET cc_start: 0.6315 (tpt) cc_final: 0.5741 (tpt) REVERT: H 6 GLU cc_start: 0.6249 (mp0) cc_final: 0.6037 (mp0) REVERT: H 28 THR cc_start: 0.8724 (p) cc_final: 0.8452 (m) REVERT: H 46 GLU cc_start: 0.7785 (tt0) cc_final: 0.7491 (pt0) REVERT: H 81 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7635 (ttmm) REVERT: Q 172 MET cc_start: 0.8402 (tpp) cc_final: 0.8154 (tpt) REVERT: Q 186 THR cc_start: 0.9126 (m) cc_final: 0.8838 (p) REVERT: Q 221 ASP cc_start: 0.7618 (t0) cc_final: 0.7259 (t70) REVERT: R 571 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.4607 (mt) REVERT: R 668 MET cc_start: 0.5657 (tpt) cc_final: 0.5170 (tpp) REVERT: T 69 THR cc_start: 0.8134 (p) cc_final: 0.7888 (p) REVERT: T 79 GLN cc_start: 0.8133 (mm110) cc_final: 0.7919 (mm110) REVERT: 6 221 ASP cc_start: 0.7244 (t0) cc_final: 0.6808 (t70) REVERT: 7 545 MET cc_start: 0.7055 (mtp) cc_final: 0.6578 (mtp) REVERT: 7 667 ASN cc_start: 0.6887 (m-40) cc_final: 0.6488 (t0) REVERT: 7 668 MET cc_start: 0.6067 (tpt) cc_final: 0.5566 (tpp) REVERT: 8 64 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8166 (mmmt) REVERT: 8 77 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7084 (mm-40) outliers start: 47 outliers final: 36 residues processed: 276 average time/residue: 0.3523 time to fit residues: 153.6182 Evaluate side-chains 257 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain R residue 571 LEU Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 28 THR Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 151 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN ** R 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 ASN S 105 GLN 9 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.180999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.145908 restraints weight = 31954.800| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.15 r_work: 0.3538 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23580 Z= 0.169 Angle : 0.664 9.106 32343 Z= 0.325 Chirality : 0.045 0.288 3993 Planarity : 0.004 0.056 3801 Dihedral : 7.634 60.000 6108 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.92 % Favored : 93.53 % Rotamer: Outliers : 1.77 % Allowed : 13.51 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2583 helix: 2.03 (0.24), residues: 453 sheet: -0.14 (0.19), residues: 711 loop : -1.43 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 345 HIS 0.003 0.001 HIS 6 364 PHE 0.028 0.002 PHE 6 346 TYR 0.021 0.001 TYR A 401 ARG 0.013 0.001 ARG 7 594 Details of bonding type rmsd link_TRANS : bond 0.00126 ( 9) link_TRANS : angle 0.41022 ( 27) link_NAG-ASN : bond 0.00334 ( 75) link_NAG-ASN : angle 2.04070 ( 225) link_ALPHA1-6 : bond 0.00751 ( 12) link_ALPHA1-6 : angle 1.64667 ( 36) link_BETA1-4 : bond 0.00478 ( 48) link_BETA1-4 : angle 1.34354 ( 144) link_ALPHA1-2 : bond 0.00354 ( 6) link_ALPHA1-2 : angle 1.54461 ( 18) link_ALPHA1-3 : bond 0.01154 ( 12) link_ALPHA1-3 : angle 1.78409 ( 36) hydrogen bonds : bond 0.04034 ( 780) hydrogen bonds : angle 5.23745 ( 2007) link_BETA1-6 : bond 0.00529 ( 9) link_BETA1-6 : angle 1.14863 ( 27) SS BOND : bond 0.00608 ( 33) SS BOND : angle 1.15935 ( 66) covalent geometry : bond 0.00401 (23376) covalent geometry : angle 0.63187 (31764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5166 Ramachandran restraints generated. 2583 Oldfield, 0 Emsley, 2583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8542 (tp40) cc_final: 0.8327 (mm-40) REVERT: B 590 ASN cc_start: 0.4926 (m-40) cc_final: 0.4679 (t0) REVERT: B 609 ASN cc_start: 0.7281 (m-40) cc_final: 0.7017 (m-40) REVERT: B 668 MET cc_start: 0.6167 (tpt) cc_final: 0.5611 (tpt) REVERT: H 28 THR cc_start: 0.8788 (p) cc_final: 0.8529 (m) REVERT: H 81 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7677 (ttmm) REVERT: Q 172 MET cc_start: 0.8470 (tpp) cc_final: 0.8203 (tpt) REVERT: Q 186 THR cc_start: 0.9147 (m) cc_final: 0.8862 (p) REVERT: Q 221 ASP cc_start: 0.7672 (t0) cc_final: 0.7287 (t70) REVERT: R 668 MET cc_start: 0.5792 (tpt) cc_final: 0.5262 (tpp) REVERT: T 69 THR cc_start: 0.8230 (p) cc_final: 0.7965 (p) REVERT: 6 95 GLU cc_start: 0.8257 (tp30) cc_final: 0.7788 (tp30) REVERT: 6 221 ASP cc_start: 0.7450 (t0) cc_final: 0.6977 (t70) REVERT: 7 667 ASN cc_start: 0.6893 (m-40) cc_final: 0.6499 (t0) REVERT: 7 668 MET cc_start: 0.6149 (tpt) cc_final: 0.5644 (tpp) REVERT: 8 13 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7416 (mmm160) REVERT: 8 64 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8230 (mmmt) outliers start: 41 outliers final: 36 residues processed: 270 average time/residue: 0.3286 time to fit residues: 141.4081 Evaluate side-chains 262 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 378 LEU Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 28 THR Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 234 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 592 GLN R 672 GLN S 56 ASN S 82AASN S 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.178559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141940 restraints weight = 31844.867| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.53 r_work: 0.3493 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 23580 Z= 0.206 Angle : 0.694 8.336 32343 Z= 0.342 Chirality : 0.045 0.289 3993 Planarity : 0.005 0.060 3801 Dihedral : 7.556 59.561 6108 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.58 % Favored : 92.95 % Rotamer: Outliers : 1.73 % Allowed : 13.85 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2583 helix: 1.99 (0.24), residues: 453 sheet: -0.27 (0.20), residues: 690 loop : -1.57 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Q 345 HIS 0.004 0.001 HIS Q 364 PHE 0.024 0.002 PHE 6 346 TYR 0.025 0.002 TYR 6 401 ARG 0.012 0.001 ARG 7 594 Details of bonding type rmsd link_TRANS : bond 0.00182 ( 9) link_TRANS : angle 0.44389 ( 27) link_NAG-ASN : bond 0.00341 ( 75) link_NAG-ASN : angle 2.07614 ( 225) link_ALPHA1-6 : bond 0.00574 ( 12) link_ALPHA1-6 : angle 1.64514 ( 36) link_BETA1-4 : bond 0.00480 ( 48) link_BETA1-4 : angle 1.41844 ( 144) link_ALPHA1-2 : bond 0.00292 ( 6) link_ALPHA1-2 : angle 1.58852 ( 18) link_ALPHA1-3 : bond 0.01106 ( 12) link_ALPHA1-3 : angle 1.78512 ( 36) hydrogen bonds : bond 0.04183 ( 780) hydrogen bonds : angle 5.35528 ( 2007) link_BETA1-6 : bond 0.00484 ( 9) link_BETA1-6 : angle 1.16116 ( 27) SS BOND : bond 0.00660 ( 33) SS BOND : angle 1.30016 ( 66) covalent geometry : bond 0.00495 (23376) covalent geometry : angle 0.66137 (31764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11807.95 seconds wall clock time: 209 minutes 0.09 seconds (12540.09 seconds total)