Starting phenix.real_space_refine on Sat Jul 4 19:45:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_25621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_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 { model { file = "/net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_25621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_25621.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_25621.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_25621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_25621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2p_25621/07_2026/7t2p_25621.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.049 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 4.81, per 1000 atoms: 0.21 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: 1.77 Conformation dependent library (CDL) restraints added in 878.2 milliseconds 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: 0.70 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: 3.04 Time building geometry restraints manager: 2.37 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 - 15.08: 12111 15.08 - 30.16: 426 30.16 - 45.25: 138 45.25 - 60.33: 72 60.33 - 75.41: 18 Dihedral angle restraints: 12765 sinusoidal: 5142 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 12762 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: 0.06 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.610 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 10.256 75.408 7731 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (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 ARG 0.011 0.001 ARG 6 231 TYR 0.057 0.009 TYR H 91 PHE 0.049 0.008 PHE R 537 TRP 0.048 0.008 TRP A 290 HIS 0.008 0.002 HIS S 100N Details of bonding type rmsd/Z covalent geometry : bond 0.02258 / 1.17 (23376) covalent geometry : angle 1.85451 / 1.18 (31764) SS BOND : bond 0.07562 / 3.38 ( 33) SS BOND : angle 2.85578 / 1.86 ( 66) hydrogen bonds : bond 0.18789 / 12.50 ( 780) hydrogen bonds : angle 7.59337 / 5.26 ( 2007) link_ALPHA1-2 : bond 0.08532 / 4.61 ( 6) link_ALPHA1-2 : angle 4.13134 / 2.14 ( 18) link_ALPHA1-3 : bond 0.08691 / 5.54 ( 12) link_ALPHA1-3 : angle 4.47246 / 2.66 ( 36) link_ALPHA1-6 : bond 0.05477 / 3.50 ( 12) link_ALPHA1-6 : angle 3.74196 / 2.18 ( 36) link_BETA1-4 : bond 0.07212 / 4.66 ( 48) link_BETA1-4 : angle 4.44336 / 3.03 ( 144) link_BETA1-6 : bond 0.05504 / 3.25 ( 9) link_BETA1-6 : angle 2.93748 / 1.91 ( 27) link_NAG-ASN : bond 0.07841 / 4.83 ( 75) link_NAG-ASN : angle 2.82176 / 2.02 ( 225) link_TRANS : bond 0.00559 / 0.37 ( 9) link_TRANS : angle 1.58406 / 0.97 ( 27) *********************** 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 : 0.655 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: 0.7088 (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: 0.6336 (t) REVERT: B 563 ILE cc_start: 0.7776 (mt) cc_final: 0.7405 (tp) REVERT: B 567 GLN cc_start: 0.7095 (mt0) cc_final: 0.5883 (mt0) REVERT: B 590 ASN cc_start: 0.5725 (m-40) cc_final: 0.5142 (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: 0.7927 (tpt) REVERT: Q 205 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: Q 306 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6918 (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: 0.8262 (mt) REVERT: R 553 THR cc_start: 0.6820 (p) cc_final: 0.6597 (t) REVERT: R 590 ASN cc_start: 0.5176 (m-40) cc_final: 0.4623 (t0) REVERT: R 668 MET cc_start: 0.6390 (tpp) cc_final: 0.5543 (mmp) REVERT: S 21 THR cc_start: 0.8219 (m) cc_final: 0.7836 (p) REVERT: S 32 CYS cc_start: 0.6893 (t) cc_final: 0.6648 (p) REVERT: S 69 ILE cc_start: 0.7347 (mt) cc_final: 0.7031 (mt) REVERT: S 73 MET cc_start: 0.7020 (mtt) cc_final: 0.6717 (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: 0.7290 (mmt-90) REVERT: 7 553 THR cc_start: 0.6745 (p) cc_final: 0.6470 (t) REVERT: 7 590 ASN cc_start: 0.5115 (m-40) cc_final: 0.4513 (t0) REVERT: 7 611 TRP cc_start: 0.7438 (m-10) cc_final: 0.7214 (m-10) REVERT: 7 625 TRP cc_start: 0.7239 (t-100) cc_final: 0.6997 (t-100) REVERT: 7 667 ASN cc_start: 0.7015 (m-40) cc_final: 0.6577 (t0) outliers start: 9 outliers final: 0 residues processed: 515 average time/residue: 0.1589 time to fit residues: 123.7067 Evaluate side-chains 270 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 264 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 56 ASN S 77 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107760 restraints weight = 30191.374| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.95 r_work: 0.3193 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23580 Z= 0.187 Angle : 0.837 12.597 32343 Z= 0.418 Chirality : 0.048 0.378 3993 Planarity : 0.005 0.052 3801 Dihedral : 5.788 39.050 2844 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.56 % Favored : 95.97 % Rotamer: Outliers : 1.56 % Allowed : 7.36 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2583 helix: 1.31 (0.24), residues: 438 sheet: 0.30 (0.17), residues: 744 loop : -0.61 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 313 TYR 0.020 0.002 TYR 8 90 PHE 0.023 0.002 PHE R 537 TRP 0.031 0.002 TRP R 625 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (23376) covalent geometry : angle 0.78968 / 0.41 (31764) SS BOND : bond 0.00298 / 0.17 ( 33) SS BOND : angle 0.78864 / 0.54 ( 66) hydrogen bonds : bond 0.06504 / 4.43 ( 780) hydrogen bonds : angle 6.14236 / 4.19 ( 2007) link_ALPHA1-2 : bond 0.00116 / 0.06 ( 6) link_ALPHA1-2 : angle 1.97975 / 1.16 ( 18) link_ALPHA1-3 : bond 0.00855 / 0.53 ( 12) link_ALPHA1-3 : angle 1.43139 / 0.86 ( 36) link_ALPHA1-6 : bond 0.00431 / 0.27 ( 12) link_ALPHA1-6 : angle 1.47023 / 0.90 ( 36) link_BETA1-4 : bond 0.00689 / 0.42 ( 48) link_BETA1-4 : angle 2.31826 / 1.58 ( 144) link_BETA1-6 : bond 0.00826 / 0.53 ( 9) link_BETA1-6 : angle 0.90435 / 0.55 ( 27) link_NAG-ASN : bond 0.00624 / 0.37 ( 75) link_NAG-ASN : angle 2.79106 / 1.96 ( 225) link_TRANS : bond 0.00109 / 0.06 ( 9) link_TRANS : angle 0.74738 / 0.48 ( 27) *********************** 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 383 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 347 time to evaluate : 0.752 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: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.7606 (mttt) cc_final: 0.7398 (mtpt) REVERT: A 290 TRP cc_start: 0.8299 (m100) cc_final: 0.8095 (m100) REVERT: A 324 ILE cc_start: 0.8436 (pt) cc_final: 0.8235 (pt) REVERT: B 553 THR cc_start: 0.6253 (p) cc_final: 0.5717 (t) REVERT: B 563 ILE cc_start: 0.7582 (mt) cc_final: 0.7115 (tp) REVERT: B 567 GLN cc_start: 0.6521 (mt0) cc_final: 0.6280 (mt0) REVERT: B 641 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7302 (mp0) REVERT: B 668 MET cc_start: 0.6311 (tpt) cc_final: 0.5997 (tpp) REVERT: H 6 GLU cc_start: 0.5838 (mp0) cc_final: 0.5511 (mp0) REVERT: H 21 THR cc_start: 0.7748 (m) cc_final: 0.7527 (p) REVERT: H 55 ASP cc_start: 0.8056 (m-30) cc_final: 0.7774 (m-30) REVERT: L 39 LYS cc_start: 0.7459 (mmmt) cc_final: 0.7076 (mmtm) REVERT: L 91 TYR cc_start: 0.8136 (p90) cc_final: 0.7748 (p90) REVERT: Q 95 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7647 (tp30) REVERT: Q 172 MET cc_start: 0.8406 (tpp) cc_final: 0.8178 (tpt) REVERT: Q 193 VAL cc_start: 0.8689 (t) cc_final: 0.8488 (m) REVERT: R 631 ILE cc_start: 0.7973 (tp) cc_final: 0.7680 (mt) REVERT: R 641 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7331 (mp0) REVERT: S 5 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8121 (tp-100) REVERT: 6 95 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7570 (tp30) REVERT: 6 257 LYS cc_start: 0.8052 (mttt) cc_final: 0.7681 (mtpt) REVERT: 6 281 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8115 (mtp-110) REVERT: 6 325 MET cc_start: 0.8375 (mtm) cc_final: 0.8105 (mtp) REVERT: 7 553 THR cc_start: 0.6772 (p) cc_final: 0.6276 (t) REVERT: 7 625 TRP cc_start: 0.7286 (t-100) cc_final: 0.6649 (t-100) REVERT: 7 667 ASN cc_start: 0.6916 (m-40) cc_final: 0.6515 (t0) REVERT: 7 668 MET cc_start: 0.6259 (tpt) cc_final: 0.5573 (tpp) REVERT: 8 6 GLU cc_start: 0.5650 (mp0) cc_final: 0.5350 (mp0) REVERT: 8 69 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6831 (mt) REVERT: 8 72 ASP cc_start: 0.7015 (t0) cc_final: 0.6809 (t0) REVERT: 9 104 LEU cc_start: 0.5890 (tp) cc_final: 0.5514 (tp) outliers start: 36 outliers final: 23 residues processed: 375 average time/residue: 0.1554 time to fit residues: 91.7753 Evaluate side-chains 299 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 275 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 S residue 87 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 69 ILE Chi-restraints excluded: chain 8 residue 87 THR Chi-restraints excluded: chain 9 residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 567 GLN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 223 HIS ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 ASN S 82AASN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107732 restraints weight = 31116.212| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.77 r_work: 0.3045 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23580 Z= 0.204 Angle : 0.752 12.848 32343 Z= 0.374 Chirality : 0.046 0.322 3993 Planarity : 0.005 0.044 3801 Dihedral : 5.391 31.849 2832 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.72 % Favored : 94.81 % Rotamer: Outliers : 2.12 % Allowed : 9.09 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2583 helix: 1.03 (0.23), residues: 453 sheet: 0.12 (0.19), residues: 663 loop : -1.04 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 594 TYR 0.029 0.002 TYR 6 401 PHE 0.021 0.003 PHE A 330 TRP 0.029 0.002 TRP 6 91 HIS 0.004 0.001 HIS Q 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (23376) covalent geometry : angle 0.71726 / 0.37 (31764) SS BOND : bond 0.00493 / 0.31 ( 33) SS BOND : angle 0.95149 / 0.63 ( 66) hydrogen bonds : bond 0.05231 / 3.53 ( 780) hydrogen bonds : angle 5.75817 / 3.95 ( 2007) link_ALPHA1-2 : bond 0.00256 / 0.14 ( 6) link_ALPHA1-2 : angle 1.59918 / 0.92 ( 18) link_ALPHA1-3 : bond 0.00788 / 0.50 ( 12) link_ALPHA1-3 : angle 1.59733 / 0.94 ( 36) link_ALPHA1-6 : bond 0.00507 / 0.32 ( 12) link_ALPHA1-6 : angle 1.41028 / 0.85 ( 36) link_BETA1-4 : bond 0.00582 / 0.36 ( 48) link_BETA1-4 : angle 1.71841 / 1.18 ( 144) link_BETA1-6 : bond 0.00553 / 0.33 ( 9) link_BETA1-6 : angle 1.08536 / 0.64 ( 27) link_NAG-ASN : bond 0.00428 / 0.26 ( 75) link_NAG-ASN : angle 2.32500 / 1.65 ( 225) link_TRANS : bond 0.00157 / 0.10 ( 9) link_TRANS : angle 0.50317 / 0.31 ( 27) *********************** 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 331 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 282 time to evaluate : 0.857 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: A 88 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 95 GLU cc_start: 0.7894 (tp30) cc_final: 0.7679 (tp30) REVERT: A 172 MET cc_start: 0.8504 (tpp) cc_final: 0.8163 (tpt) REVERT: A 290 TRP cc_start: 0.8360 (m100) cc_final: 0.8042 (m100) REVERT: A 404 MET cc_start: 0.8315 (mtp) cc_final: 0.7920 (mmm) REVERT: A 501 GLU cc_start: 0.7942 (tt0) cc_final: 0.7583 (tt0) REVERT: B 545 MET cc_start: 0.7098 (mtp) cc_final: 0.6872 (mtp) REVERT: B 553 THR cc_start: 0.6072 (p) cc_final: 0.5735 (t) REVERT: B 633 LYS cc_start: 0.7141 (mmtm) cc_final: 0.6929 (mmtm) REVERT: B 668 MET cc_start: 0.6146 (tpt) cc_final: 0.5873 (tpp) REVERT: H 6 GLU cc_start: 0.5967 (mp0) cc_final: 0.5696 (mp0) REVERT: H 55 ASP cc_start: 0.8286 (m-30) cc_final: 0.8051 (m-30) REVERT: L 91 TYR cc_start: 0.8145 (p90) cc_final: 0.7711 (p90) REVERT: Q 88 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6997 (tm-30) REVERT: Q 95 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7549 (tp30) REVERT: Q 309 MET cc_start: 0.8638 (ttt) cc_final: 0.8251 (ttt) REVERT: R 599 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7731 (mm-30) REVERT: R 631 ILE cc_start: 0.8231 (tp) cc_final: 0.7941 (mt) REVERT: R 668 MET cc_start: 0.5765 (tpt) cc_final: 0.5262 (tpp) REVERT: S 13 ARG cc_start: 0.8342 (mpt180) cc_final: 0.8067 (tpp80) REVERT: S 55 ASP cc_start: 0.8205 (m-30) cc_final: 0.7897 (m-30) REVERT: S 77 GLN cc_start: 0.7886 (mt0) cc_final: 0.7654 (mm-40) REVERT: 6 103 LYS cc_start: 0.8615 (mttt) cc_final: 0.8411 (mttp) REVERT: 6 257 LYS cc_start: 0.8135 (mttt) cc_final: 0.7767 (mtpt) REVERT: 6 309 MET cc_start: 0.8513 (ttt) cc_final: 0.8127 (ttt) REVERT: 7 553 THR cc_start: 0.6436 (p) cc_final: 0.5966 (t) REVERT: 7 667 ASN cc_start: 0.6968 (m-40) cc_final: 0.6561 (t0) REVERT: 7 668 MET cc_start: 0.6295 (tpt) cc_final: 0.5469 (tpp) REVERT: 8 72 ASP cc_start: 0.6866 (t0) cc_final: 0.6619 (t0) REVERT: 8 105 GLN cc_start: 0.8616 (mm110) cc_final: 0.8190 (tm-30) REVERT: 9 104 LEU cc_start: 0.6147 (tp) cc_final: 0.5627 (tt) outliers start: 49 outliers final: 31 residues processed: 318 average time/residue: 0.1595 time to fit residues: 79.3240 Evaluate side-chains 275 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 100 ASN Chi-restraints excluded: chain H residue 107 VAL 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 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 S residue 100 ASN Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 72 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 345 TRP 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 9 residue 3 LEU Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 170 optimal weight: 5.9990 chunk 236 optimal weight: 0.0060 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 640 GLN S 82AASN 7 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108859 restraints weight = 30980.883| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.88 r_work: 0.3056 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3807 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= 0.160 Angle : 0.679 9.649 32343 Z= 0.339 Chirality : 0.043 0.314 3993 Planarity : 0.004 0.054 3801 Dihedral : 5.223 29.746 2830 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.84 % Favored : 94.73 % Rotamer: Outliers : 2.29 % Allowed : 10.00 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2583 helix: 1.41 (0.24), residues: 453 sheet: 0.03 (0.19), residues: 663 loop : -1.12 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 594 TYR 0.021 0.001 TYR 6 401 PHE 0.017 0.002 PHE 7 537 TRP 0.025 0.001 TRP 6 91 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (23376) covalent geometry : angle 0.64252 / 0.33 (31764) SS BOND : bond 0.00349 / 0.23 ( 33) SS BOND : angle 1.38190 / 1.12 ( 66) hydrogen bonds : bond 0.04599 / 3.12 ( 780) hydrogen bonds : angle 5.53952 / 3.79 ( 2007) link_ALPHA1-2 : bond 0.00205 / 0.11 ( 6) link_ALPHA1-2 : angle 1.61981 / 0.94 ( 18) link_ALPHA1-3 : bond 0.00678 / 0.43 ( 12) link_ALPHA1-3 : angle 1.45135 / 0.87 ( 36) link_ALPHA1-6 : bond 0.00454 / 0.29 ( 12) link_ALPHA1-6 : angle 1.41841 / 0.85 ( 36) link_BETA1-4 : bond 0.00503 / 0.31 ( 48) link_BETA1-4 : angle 1.53507 / 1.06 ( 144) link_BETA1-6 : bond 0.00628 / 0.38 ( 9) link_BETA1-6 : angle 1.05002 / 0.62 ( 27) link_NAG-ASN : bond 0.00365 / 0.22 ( 75) link_NAG-ASN : angle 2.21123 / 1.56 ( 225) link_TRANS : bond 0.00124 / 0.08 ( 9) link_TRANS : angle 0.46543 / 0.29 ( 27) *********************** 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 331 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 0.880 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: A 40 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 92 GLN cc_start: 0.8219 (tp40) cc_final: 0.7777 (tp40) REVERT: A 257 LYS cc_start: 0.7644 (mttt) cc_final: 0.7439 (mtpt) REVERT: A 290 TRP cc_start: 0.8311 (m100) cc_final: 0.7974 (m100) REVERT: A 309 MET cc_start: 0.8396 (ttp) cc_final: 0.8079 (ttt) REVERT: A 404 MET cc_start: 0.8311 (mtp) cc_final: 0.8110 (mmm) REVERT: A 501 GLU cc_start: 0.8001 (tt0) cc_final: 0.7729 (tt0) REVERT: B 553 THR cc_start: 0.5804 (p) cc_final: 0.5511 (t) REVERT: B 599 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: B 633 LYS cc_start: 0.6917 (mmtm) cc_final: 0.6673 (mmtm) REVERT: B 668 MET cc_start: 0.6164 (tpt) cc_final: 0.5668 (tpt) REVERT: H 6 GLU cc_start: 0.5941 (mp0) cc_final: 0.5629 (mp0) REVERT: H 55 ASP cc_start: 0.8367 (m-30) cc_final: 0.8122 (m-30) REVERT: L 91 TYR cc_start: 0.8112 (p90) cc_final: 0.7628 (p90) REVERT: Q 88 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6885 (tm-30) REVERT: Q 91 TRP cc_start: 0.6981 (t-100) cc_final: 0.6696 (t-100) REVERT: Q 95 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7546 (tp30) REVERT: Q 290 TRP cc_start: 0.8389 (m100) cc_final: 0.8058 (m100) REVERT: Q 309 MET cc_start: 0.8519 (ttt) cc_final: 0.8154 (ttt) REVERT: R 631 ILE cc_start: 0.8108 (tp) cc_final: 0.7881 (mt) REVERT: R 668 MET cc_start: 0.5657 (tpt) cc_final: 0.5087 (tpp) REVERT: S 13 ARG cc_start: 0.8261 (mpt180) cc_final: 0.8036 (tpp-160) REVERT: S 46 GLU cc_start: 0.7840 (tt0) cc_final: 0.7451 (pt0) REVERT: S 55 ASP cc_start: 0.8276 (m-30) cc_final: 0.8022 (m-30) REVERT: S 94 ARG cc_start: 0.7178 (mmm-85) cc_final: 0.6948 (mmm-85) REVERT: T 33 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8543 (tp) REVERT: 6 91 TRP cc_start: 0.6862 (t-100) cc_final: 0.6207 (t-100) REVERT: 6 95 GLU cc_start: 0.7547 (tp30) cc_final: 0.6855 (tp30) REVERT: 6 103 LYS cc_start: 0.8831 (mttt) cc_final: 0.8579 (mttp) REVERT: 6 221 ASP cc_start: 0.8290 (t0) cc_final: 0.7905 (t0) REVERT: 6 257 LYS cc_start: 0.8003 (mttt) cc_final: 0.7650 (mtpt) REVERT: 6 290 TRP cc_start: 0.8362 (m100) cc_final: 0.8058 (m100) REVERT: 6 309 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8135 (ttt) REVERT: 7 545 MET cc_start: 0.6839 (mtp) cc_final: 0.6399 (mtp) REVERT: 7 667 ASN cc_start: 0.6949 (m-40) cc_final: 0.6575 (t0) REVERT: 7 668 MET cc_start: 0.6217 (tpt) cc_final: 0.5699 (tpp) REVERT: 8 32 CYS cc_start: 0.7119 (p) cc_final: 0.6783 (m) REVERT: 8 72 ASP cc_start: 0.6837 (t0) cc_final: 0.6576 (t0) REVERT: 8 94 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7312 (mmm-85) REVERT: 9 42 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8461 (pttm) REVERT: 9 104 LEU cc_start: 0.6052 (tp) cc_final: 0.5408 (tt) outliers start: 53 outliers final: 36 residues processed: 319 average time/residue: 0.1641 time to fit residues: 81.4108 Evaluate side-chains 286 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 641 GLU 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 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 438 ILE Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 37 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN H 100NHIS S 77 GLN S 82AASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107018 restraints weight = 31007.114| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.71 r_work: 0.3048 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4086 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= 0.178 Angle : 0.673 8.123 32343 Z= 0.336 Chirality : 0.043 0.315 3993 Planarity : 0.004 0.049 3801 Dihedral : 5.201 31.559 2830 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.57 % Favored : 93.96 % Rotamer: Outliers : 2.64 % Allowed : 10.78 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2583 helix: 1.86 (0.24), residues: 435 sheet: -0.04 (0.20), residues: 666 loop : -1.25 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 594 TYR 0.024 0.001 TYR 6 401 PHE 0.017 0.002 PHE 7 537 TRP 0.018 0.001 TRP 6 91 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (23376) covalent geometry : angle 0.63758 / 0.33 (31764) SS BOND : bond 0.00476 / 0.30 ( 33) SS BOND : angle 1.83243 / 1.12 ( 66) hydrogen bonds : bond 0.04442 / 3.02 ( 780) hydrogen bonds : angle 5.44035 / 3.73 ( 2007) link_ALPHA1-2 : bond 0.00217 / 0.12 ( 6) link_ALPHA1-2 : angle 1.57165 / 0.91 ( 18) link_ALPHA1-3 : bond 0.00669 / 0.43 ( 12) link_ALPHA1-3 : angle 1.49407 / 0.89 ( 36) link_ALPHA1-6 : bond 0.00404 / 0.26 ( 12) link_ALPHA1-6 : angle 1.44863 / 0.87 ( 36) link_BETA1-4 : bond 0.00479 / 0.29 ( 48) link_BETA1-4 : angle 1.46538 / 1.02 ( 144) link_BETA1-6 : bond 0.00561 / 0.34 ( 9) link_BETA1-6 : angle 1.09312 / 0.64 ( 27) link_NAG-ASN : bond 0.00347 / 0.21 ( 75) link_NAG-ASN : angle 2.08601 / 1.46 ( 225) link_TRANS : bond 0.00136 / 0.09 ( 9) link_TRANS : angle 0.41804 / 0.25 ( 27) *********************** 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 333 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 0.710 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: A 92 GLN cc_start: 0.8230 (tp40) cc_final: 0.7790 (tp40) REVERT: A 172 MET cc_start: 0.8442 (tpp) cc_final: 0.8057 (tpp) REVERT: A 290 TRP cc_start: 0.8320 (m100) cc_final: 0.8096 (m100) REVERT: A 501 GLU cc_start: 0.8012 (tt0) cc_final: 0.7794 (tt0) REVERT: B 553 THR cc_start: 0.5874 (p) cc_final: 0.5459 (t) REVERT: B 599 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: B 633 LYS cc_start: 0.7101 (mmtm) cc_final: 0.6835 (mmtm) REVERT: B 668 MET cc_start: 0.6165 (tpt) cc_final: 0.5651 (tpt) REVERT: H 32 CYS cc_start: 0.6960 (p) cc_final: 0.6497 (m) REVERT: H 55 ASP cc_start: 0.8369 (m-30) cc_final: 0.8141 (m-30) REVERT: H 72 ASP cc_start: 0.7414 (t0) cc_final: 0.7098 (t0) REVERT: H 75 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8416 (pttp) REVERT: L 39 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7399 (mmtt) REVERT: L 91 TYR cc_start: 0.8133 (p90) cc_final: 0.7693 (p90) REVERT: Q 88 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6948 (tm-30) REVERT: Q 91 TRP cc_start: 0.6910 (t-100) cc_final: 0.6503 (t-100) REVERT: Q 95 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7428 (tp30) REVERT: Q 290 TRP cc_start: 0.8370 (m100) cc_final: 0.8151 (m100) REVERT: Q 309 MET cc_start: 0.8485 (ttt) cc_final: 0.8140 (ttt) REVERT: R 668 MET cc_start: 0.5641 (tpt) cc_final: 0.5068 (tpp) REVERT: S 32 CYS cc_start: 0.6996 (p) cc_final: 0.6486 (m) REVERT: S 46 GLU cc_start: 0.7828 (tt0) cc_final: 0.7378 (pt0) REVERT: S 55 ASP cc_start: 0.8297 (m-30) cc_final: 0.8051 (m-30) REVERT: S 94 ARG cc_start: 0.7332 (mmm-85) cc_final: 0.7026 (mmm-85) REVERT: T 33 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8594 (tp) REVERT: 6 91 TRP cc_start: 0.6856 (t-100) cc_final: 0.6245 (t-100) REVERT: 6 95 GLU cc_start: 0.7627 (tp30) cc_final: 0.6943 (tp30) REVERT: 6 103 LYS cc_start: 0.8859 (mttt) cc_final: 0.8627 (mttp) REVERT: 6 221 ASP cc_start: 0.8267 (t0) cc_final: 0.7949 (t0) REVERT: 6 257 LYS cc_start: 0.8059 (mttt) cc_final: 0.7760 (mtpt) REVERT: 6 290 TRP cc_start: 0.8393 (m100) cc_final: 0.8172 (m100) REVERT: 6 309 MET cc_start: 0.8517 (ttt) cc_final: 0.8300 (ttt) REVERT: 6 482 MET cc_start: 0.9125 (mmm) cc_final: 0.8915 (mmm) REVERT: 6 501 GLU cc_start: 0.7828 (tt0) cc_final: 0.7615 (tt0) REVERT: 7 545 MET cc_start: 0.6996 (mtp) cc_final: 0.6532 (mtp) REVERT: 7 667 ASN cc_start: 0.6961 (m-40) cc_final: 0.6546 (t0) REVERT: 7 668 MET cc_start: 0.6342 (tpt) cc_final: 0.5820 (tpp) REVERT: 8 32 CYS cc_start: 0.7085 (p) cc_final: 0.6757 (m) REVERT: 8 72 ASP cc_start: 0.6908 (t0) cc_final: 0.6629 (t0) REVERT: 8 94 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.7303 (mmm-85) outliers start: 61 outliers final: 44 residues processed: 318 average time/residue: 0.1539 time to fit residues: 77.1399 Evaluate side-chains 296 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS 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 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 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 75 LYS 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 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 476 ASN Chi-restraints excluded: chain Q residue 505 ILE Chi-restraints excluded: chain R residue 595 VAL 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 220 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 107 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 64 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 0.0570 chunk 194 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN S 77 GLN S 82AASN S 100NHIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104719 restraints weight = 31583.664| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.83 r_work: 0.2983 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 23580 Z= 0.296 Angle : 0.798 9.120 32343 Z= 0.396 Chirality : 0.047 0.308 3993 Planarity : 0.006 0.049 3801 Dihedral : 5.580 29.923 2828 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.31 % Favored : 93.15 % Rotamer: Outliers : 3.16 % Allowed : 11.90 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2583 helix: 1.65 (0.24), residues: 453 sheet: -0.42 (0.19), residues: 687 loop : -1.64 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 366 TYR 0.037 0.002 TYR 6 401 PHE 0.024 0.003 PHE A 330 TRP 0.022 0.002 TRP Q 345 HIS 0.004 0.001 HIS Q 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.30 (23376) covalent geometry : angle 0.76511 / 0.39 (31764) SS BOND : bond 0.00742 / 0.50 ( 33) SS BOND : angle 1.95101 / 1.21 ( 66) hydrogen bonds : bond 0.04948 / 3.34 ( 780) hydrogen bonds : angle 5.70136 / 3.93 ( 2007) link_ALPHA1-2 : bond 0.00123 / 0.06 ( 6) link_ALPHA1-2 : angle 1.62892 / 0.95 ( 18) link_ALPHA1-3 : bond 0.00589 / 0.38 ( 12) link_ALPHA1-3 : angle 1.62608 / 0.99 ( 36) link_ALPHA1-6 : bond 0.00331 / 0.22 ( 12) link_ALPHA1-6 : angle 1.55078 / 0.93 ( 36) link_BETA1-4 : bond 0.00466 / 0.29 ( 48) link_BETA1-4 : angle 1.57685 / 1.08 ( 144) link_BETA1-6 : bond 0.00376 / 0.20 ( 9) link_BETA1-6 : angle 1.22423 / 0.73 ( 27) link_NAG-ASN : bond 0.00472 / 0.31 ( 75) link_NAG-ASN : angle 2.24048 / 1.57 ( 225) link_TRANS : bond 0.00264 / 0.18 ( 9) link_TRANS : angle 0.52402 / 0.32 ( 27) *********************** 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 332 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 259 time to evaluate : 0.851 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 88 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7162 (tm-30) REVERT: A 501 GLU cc_start: 0.8016 (tt0) cc_final: 0.7808 (tt0) REVERT: B 553 THR cc_start: 0.6112 (p) cc_final: 0.5779 (t) REVERT: B 599 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: B 633 LYS cc_start: 0.7624 (mmtm) cc_final: 0.7362 (mmtm) REVERT: B 668 MET cc_start: 0.6328 (tpt) cc_final: 0.5802 (tpt) REVERT: H 32 CYS cc_start: 0.6982 (p) cc_final: 0.6563 (m) REVERT: H 94 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7186 (mmm-85) REVERT: L 47 LEU cc_start: 0.8011 (mt) cc_final: 0.7717 (mt) REVERT: L 91 TYR cc_start: 0.8302 (p90) cc_final: 0.7991 (p90) REVERT: Q 88 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7216 (tm-30) REVERT: Q 221 ASP cc_start: 0.8080 (t0) cc_final: 0.7575 (t70) REVERT: Q 309 MET cc_start: 0.8539 (ttt) cc_final: 0.8252 (ttt) REVERT: R 668 MET cc_start: 0.5821 (tpt) cc_final: 0.5254 (tpp) REVERT: S 27 ASP cc_start: 0.8265 (t0) cc_final: 0.8014 (t70) REVERT: S 28 THR cc_start: 0.8713 (p) cc_final: 0.8497 (m) REVERT: S 32 CYS cc_start: 0.7141 (p) cc_final: 0.6746 (m) REVERT: S 46 GLU cc_start: 0.8007 (tt0) cc_final: 0.7531 (pt0) REVERT: S 55 ASP cc_start: 0.8416 (m-30) cc_final: 0.8173 (m-30) REVERT: S 94 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7216 (mmm-85) REVERT: T 69 THR cc_start: 0.8257 (p) cc_final: 0.8038 (p) REVERT: 6 91 TRP cc_start: 0.7061 (t-100) cc_final: 0.6309 (t-100) REVERT: 6 95 GLU cc_start: 0.7875 (tp30) cc_final: 0.7265 (tp30) REVERT: 6 221 ASP cc_start: 0.8252 (t0) cc_final: 0.7943 (t0) REVERT: 7 668 MET cc_start: 0.6477 (tpt) cc_final: 0.5874 (tpp) REVERT: 8 32 CYS cc_start: 0.7174 (p) cc_final: 0.6926 (m) REVERT: 8 72 ASP cc_start: 0.7315 (t0) cc_final: 0.6856 (t0) REVERT: 8 94 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: 9 69 THR cc_start: 0.8182 (p) cc_final: 0.7909 (p) outliers start: 73 outliers final: 56 residues processed: 311 average time/residue: 0.1622 time to fit residues: 80.4312 Evaluate side-chains 296 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 216 ILE 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 393 THR Chi-restraints excluded: chain A residue 411 VAL 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 599 GLU 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 40 ILE Chi-restraints excluded: chain Q residue 46 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 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain Q residue 411 VAL Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 630 LEU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 67 MET 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 216 ILE Chi-restraints excluded: chain 6 residue 220 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 393 THR 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 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 5 THR 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 241 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 39 optimal weight: 0.0000 chunk 116 optimal weight: 0.5980 chunk 212 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN B 640 GLN H 77 GLN S 77 GLN S 82AASN T 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109612 restraints weight = 31064.513| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.75 r_work: 0.3064 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 23580 Z= 0.126 Angle : 0.622 8.043 32343 Z= 0.311 Chirality : 0.042 0.291 3993 Planarity : 0.004 0.049 3801 Dihedral : 5.038 27.626 2826 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.07 % Favored : 94.39 % Rotamer: Outliers : 1.99 % Allowed : 13.77 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2583 helix: 1.81 (0.24), residues: 453 sheet: -0.23 (0.19), residues: 705 loop : -1.43 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 594 TYR 0.025 0.001 TYR T 91 PHE 0.016 0.002 PHE 7 537 TRP 0.020 0.001 TRP Q 91 HIS 0.002 0.001 HIS Q 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (23376) covalent geometry : angle 0.59307 / 0.31 (31764) SS BOND : bond 0.00337 / 0.24 ( 33) SS BOND : angle 0.98161 / 0.64 ( 66) hydrogen bonds : bond 0.04024 / 2.74 ( 780) hydrogen bonds : angle 5.36325 / 3.69 ( 2007) link_ALPHA1-2 : bond 0.00254 / 0.14 ( 6) link_ALPHA1-2 : angle 1.53775 / 0.88 ( 18) link_ALPHA1-3 : bond 0.00698 / 0.45 ( 12) link_ALPHA1-3 : angle 1.45090 / 0.87 ( 36) link_ALPHA1-6 : bond 0.00380 / 0.24 ( 12) link_ALPHA1-6 : angle 1.42908 / 0.85 ( 36) link_BETA1-4 : bond 0.00472 / 0.29 ( 48) link_BETA1-4 : angle 1.29310 / 0.90 ( 144) link_BETA1-6 : bond 0.00602 / 0.36 ( 9) link_BETA1-6 : angle 1.07406 / 0.64 ( 27) link_NAG-ASN : bond 0.00338 / 0.19 ( 75) link_NAG-ASN : angle 1.89549 / 1.34 ( 225) link_TRANS : bond 0.00091 / 0.06 ( 9) link_TRANS : angle 0.45817 / 0.29 ( 27) *********************** 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 323 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: B 553 THR cc_start: 0.5978 (p) cc_final: 0.5570 (t) REVERT: B 633 LYS cc_start: 0.7307 (mmtm) cc_final: 0.7063 (mmtm) REVERT: B 668 MET cc_start: 0.6283 (tpt) cc_final: 0.5653 (tpp) REVERT: H 32 CYS cc_start: 0.6897 (p) cc_final: 0.6546 (m) REVERT: Q 88 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7053 (tm-30) REVERT: Q 221 ASP cc_start: 0.7671 (t0) cc_final: 0.7229 (t70) REVERT: Q 309 MET cc_start: 0.8366 (ttt) cc_final: 0.8132 (ttt) REVERT: Q 502 ILE cc_start: 0.8342 (mt) cc_final: 0.8091 (mm) REVERT: R 668 MET cc_start: 0.5700 (tpt) cc_final: 0.5164 (tpp) REVERT: S 32 CYS cc_start: 0.6953 (p) cc_final: 0.6605 (m) REVERT: S 46 GLU cc_start: 0.8006 (tt0) cc_final: 0.7762 (pt0) REVERT: S 55 ASP cc_start: 0.8277 (m-30) cc_final: 0.8045 (m-30) REVERT: S 94 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.7094 (mmm-85) REVERT: T 69 THR cc_start: 0.8198 (p) cc_final: 0.7953 (p) REVERT: 6 91 TRP cc_start: 0.7007 (t-100) cc_final: 0.6428 (t-100) REVERT: 6 95 GLU cc_start: 0.7738 (tp30) cc_final: 0.7077 (tp30) REVERT: 6 221 ASP cc_start: 0.8217 (t0) cc_final: 0.7953 (t0) REVERT: 6 257 LYS cc_start: 0.8118 (mttt) cc_final: 0.7838 (mtpt) REVERT: 6 485 GLU cc_start: 0.7850 (tp30) cc_final: 0.7554 (mm-30) REVERT: 7 668 MET cc_start: 0.6537 (tpt) cc_final: 0.5946 (tpp) REVERT: 9 69 THR cc_start: 0.8137 (p) cc_final: 0.7880 (p) outliers start: 46 outliers final: 34 residues processed: 309 average time/residue: 0.1658 time to fit residues: 80.4110 Evaluate side-chains 282 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 293 ARG 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 Q residue 46 THR 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 293 ARG 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 630 LEU Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 67 MET Chi-restraints excluded: chain 6 residue 98 ILE Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 203 GLU Chi-restraints excluded: chain 6 residue 220 CYS 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 21 THR Chi-restraints excluded: chain 8 residue 28 THR Chi-restraints excluded: chain 8 residue 107 VAL Chi-restraints excluded: chain 8 residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN B 672 GLN H 77 GLN L 79 GLN R 672 GLN S 77 GLN S 82AASN 8 77 GLN 9 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108266 restraints weight = 30975.708| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.64 r_work: 0.3050 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23580 Z= 0.155 Angle : 0.651 11.714 32343 Z= 0.323 Chirality : 0.042 0.290 3993 Planarity : 0.005 0.049 3801 Dihedral : 4.972 22.943 2826 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.92 % Favored : 93.57 % Rotamer: Outliers : 1.73 % Allowed : 14.50 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2583 helix: 1.88 (0.24), residues: 453 sheet: -0.26 (0.19), residues: 705 loop : -1.47 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 594 TYR 0.033 0.001 TYR L 91 PHE 0.016 0.002 PHE 7 537 TRP 0.023 0.001 TRP Q 187 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (23376) covalent geometry : angle 0.62252 / 0.32 (31764) SS BOND : bond 0.00442 / 0.30 ( 33) SS BOND : angle 1.12597 / 0.74 ( 66) hydrogen bonds : bond 0.04113 / 2.81 ( 780) hydrogen bonds : angle 5.27963 / 3.63 ( 2007) link_ALPHA1-2 : bond 0.00249 / 0.13 ( 6) link_ALPHA1-2 : angle 1.51584 / 0.87 ( 18) link_ALPHA1-3 : bond 0.00625 / 0.40 ( 12) link_ALPHA1-3 : angle 1.49976 / 0.91 ( 36) link_ALPHA1-6 : bond 0.00331 / 0.21 ( 12) link_ALPHA1-6 : angle 1.46324 / 0.88 ( 36) link_BETA1-4 : bond 0.00452 / 0.28 ( 48) link_BETA1-4 : angle 1.30340 / 0.91 ( 144) link_BETA1-6 : bond 0.00541 / 0.31 ( 9) link_BETA1-6 : angle 1.07968 / 0.64 ( 27) link_NAG-ASN : bond 0.00313 / 0.18 ( 75) link_NAG-ASN : angle 1.93608 / 1.38 ( 225) link_TRANS : bond 0.00104 / 0.07 ( 9) link_TRANS : angle 0.41253 / 0.26 ( 27) *********************** 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 293 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 668 MET cc_start: 0.6349 (tpt) cc_final: 0.5897 (tpp) REVERT: H 32 CYS cc_start: 0.6962 (p) cc_final: 0.6612 (m) REVERT: Q 88 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6977 (tm-30) REVERT: Q 221 ASP cc_start: 0.7829 (t0) cc_final: 0.7354 (t70) REVERT: Q 309 MET cc_start: 0.8455 (ttt) cc_final: 0.8192 (ttt) REVERT: R 594 ARG cc_start: 0.6816 (ttp80) cc_final: 0.6548 (tmm160) REVERT: R 668 MET cc_start: 0.5874 (tpt) cc_final: 0.5359 (tpp) REVERT: S 32 CYS cc_start: 0.7065 (p) cc_final: 0.6763 (m) REVERT: S 46 GLU cc_start: 0.7993 (tt0) cc_final: 0.7732 (pt0) REVERT: S 55 ASP cc_start: 0.8315 (m-30) cc_final: 0.8056 (m-30) REVERT: S 94 ARG cc_start: 0.7482 (mmm-85) cc_final: 0.7104 (mmm-85) REVERT: T 69 THR cc_start: 0.8209 (p) cc_final: 0.7948 (p) REVERT: 6 91 TRP cc_start: 0.6977 (t-100) cc_final: 0.6424 (t-100) REVERT: 6 95 GLU cc_start: 0.7753 (tp30) cc_final: 0.7213 (tp30) REVERT: 6 257 LYS cc_start: 0.8138 (mttt) cc_final: 0.7853 (mtpt) REVERT: 6 485 GLU cc_start: 0.7878 (tp30) cc_final: 0.7504 (mm-30) REVERT: 7 668 MET cc_start: 0.6338 (tpt) cc_final: 0.5721 (tpp) REVERT: 8 13 ARG cc_start: 0.7943 (mmm160) cc_final: 0.7633 (mmm160) REVERT: 9 69 THR cc_start: 0.8168 (p) cc_final: 0.7909 (p) outliers start: 40 outliers final: 36 residues processed: 279 average time/residue: 0.1527 time to fit residues: 68.6761 Evaluate side-chains 272 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 335 ILE 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 28 THR 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 108 CYS Chi-restraints excluded: chain Q residue 203 GLU Chi-restraints excluded: chain Q residue 220 CYS Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 630 LEU Chi-restraints excluded: chain R residue 631 ILE Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 67 MET Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 216 ILE Chi-restraints excluded: chain 6 residue 220 CYS Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 393 THR Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 109 VAL Chi-restraints excluded: chain 9 residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 3 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 174 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 chunk 80 optimal weight: 0.0010 chunk 202 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN H 77 GLN L 30 ASN ** R 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 ASN S 77 GLN S 82AASN 7 592 GLN 8 77 GLN 8 100NHIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110652 restraints weight = 31166.517| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.60 r_work: 0.3098 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23580 Z= 0.118 Angle : 0.611 8.071 32343 Z= 0.306 Chirality : 0.041 0.285 3993 Planarity : 0.004 0.049 3801 Dihedral : 4.793 22.063 2826 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.65 % Favored : 93.88 % Rotamer: Outliers : 1.73 % Allowed : 14.81 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2583 helix: 1.89 (0.24), residues: 453 sheet: -0.16 (0.19), residues: 684 loop : -1.41 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 594 TYR 0.027 0.001 TYR L 91 PHE 0.015 0.001 PHE B 537 TRP 0.023 0.001 TRP Q 187 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (23376) covalent geometry : angle 0.58473 / 0.30 (31764) SS BOND : bond 0.00288 / 0.19 ( 33) SS BOND : angle 0.78951 / 0.52 ( 66) hydrogen bonds : bond 0.03886 / 2.68 ( 780) hydrogen bonds : angle 5.16375 / 3.54 ( 2007) link_ALPHA1-2 : bond 0.00284 / 0.15 ( 6) link_ALPHA1-2 : angle 1.48357 / 0.85 ( 18) link_ALPHA1-3 : bond 0.00670 / 0.43 ( 12) link_ALPHA1-3 : angle 1.45482 / 0.87 ( 36) link_ALPHA1-6 : bond 0.00374 / 0.23 ( 12) link_ALPHA1-6 : angle 1.43457 / 0.86 ( 36) link_BETA1-4 : bond 0.00460 / 0.28 ( 48) link_BETA1-4 : angle 1.23774 / 0.87 ( 144) link_BETA1-6 : bond 0.00584 / 0.35 ( 9) link_BETA1-6 : angle 1.08506 / 0.64 ( 27) link_NAG-ASN : bond 0.00319 / 0.19 ( 75) link_NAG-ASN : angle 1.81606 / 1.30 ( 225) link_TRANS : bond 0.00087 / 0.04 ( 9) link_TRANS : angle 0.43393 / 0.28 ( 27) *********************** 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 293 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.846 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 245 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: A 290 TRP cc_start: 0.8443 (m100) cc_final: 0.7963 (m100) REVERT: A 485 GLU cc_start: 0.7831 (tp30) cc_final: 0.7435 (mm-30) REVERT: B 668 MET cc_start: 0.6104 (tpt) cc_final: 0.5690 (tpp) REVERT: H 32 CYS cc_start: 0.6909 (p) cc_final: 0.6574 (m) REVERT: Q 88 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6896 (tm-30) REVERT: Q 186 THR cc_start: 0.9251 (m) cc_final: 0.8519 (p) REVERT: Q 221 ASP cc_start: 0.7536 (t0) cc_final: 0.7066 (t70) REVERT: Q 502 ILE cc_start: 0.8284 (mt) cc_final: 0.8041 (mm) REVERT: R 594 ARG cc_start: 0.6727 (ttp80) cc_final: 0.6435 (tmm160) REVERT: R 668 MET cc_start: 0.5818 (tpt) cc_final: 0.5312 (tpp) REVERT: S 55 ASP cc_start: 0.8269 (m-30) cc_final: 0.8025 (m-30) REVERT: S 94 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7155 (mmm-85) REVERT: T 69 THR cc_start: 0.8197 (p) cc_final: 0.7941 (p) REVERT: T 79 GLN cc_start: 0.7891 (mm110) cc_final: 0.7581 (mm110) REVERT: 6 91 TRP cc_start: 0.6887 (t-100) cc_final: 0.6395 (t-100) REVERT: 6 95 GLU cc_start: 0.7728 (tp30) cc_final: 0.7197 (tp30) REVERT: 6 257 LYS cc_start: 0.7979 (mttt) cc_final: 0.7748 (mtpt) REVERT: 6 485 GLU cc_start: 0.7789 (tp30) cc_final: 0.7529 (mm-30) REVERT: 7 668 MET cc_start: 0.6221 (tpt) cc_final: 0.5584 (tpp) REVERT: 8 64 LYS cc_start: 0.8372 (mmmm) cc_final: 0.7912 (mmmt) REVERT: 9 69 THR cc_start: 0.8130 (p) cc_final: 0.7873 (p) outliers start: 40 outliers final: 34 residues processed: 277 average time/residue: 0.1557 time to fit residues: 69.3806 Evaluate side-chains 275 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 245 ASP 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 28 THR Chi-restraints excluded: chain H residue 48 ILE 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 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 368 THR Chi-restraints excluded: chain Q residue 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain R residue 630 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 293 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 chunk 237 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN B 635 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 592 GLN S 77 GLN S 82AASN 8 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.146584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109723 restraints weight = 31012.275| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.89 r_work: 0.3060 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23580 Z= 0.149 Angle : 0.635 8.513 32343 Z= 0.317 Chirality : 0.042 0.283 3993 Planarity : 0.004 0.053 3801 Dihedral : 4.840 22.132 2826 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.92 % Favored : 93.61 % Rotamer: Outliers : 1.47 % Allowed : 15.41 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2583 helix: 1.97 (0.24), residues: 453 sheet: -0.19 (0.19), residues: 681 loop : -1.52 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 281 TYR 0.025 0.001 TYR L 91 PHE 0.015 0.002 PHE B 537 TRP 0.038 0.001 TRP Q 345 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (23376) covalent geometry : angle 0.60857 / 0.31 (31764) SS BOND : bond 0.00435 / 0.31 ( 33) SS BOND : angle 0.97114 / 0.64 ( 66) hydrogen bonds : bond 0.03994 / 2.72 ( 780) hydrogen bonds : angle 5.19183 / 3.56 ( 2007) link_ALPHA1-2 : bond 0.00274 / 0.15 ( 6) link_ALPHA1-2 : angle 1.49483 / 0.86 ( 18) link_ALPHA1-3 : bond 0.00622 / 0.40 ( 12) link_ALPHA1-3 : angle 1.49536 / 0.90 ( 36) link_ALPHA1-6 : bond 0.00336 / 0.22 ( 12) link_ALPHA1-6 : angle 1.46878 / 0.89 ( 36) link_BETA1-4 : bond 0.00439 / 0.27 ( 48) link_BETA1-4 : angle 1.25402 / 0.88 ( 144) link_BETA1-6 : bond 0.00511 / 0.30 ( 9) link_BETA1-6 : angle 1.10648 / 0.66 ( 27) link_NAG-ASN : bond 0.00294 / 0.17 ( 75) link_NAG-ASN : angle 1.82179 / 1.29 ( 225) link_TRANS : bond 0.00096 / 0.06 ( 9) link_TRANS : angle 0.40406 / 0.26 ( 27) ********************** 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: 34 poor density : 242 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: A 290 TRP cc_start: 0.8494 (m100) cc_final: 0.8030 (m100) REVERT: A 485 GLU cc_start: 0.7881 (tp30) cc_final: 0.7433 (mm-30) REVERT: B 668 MET cc_start: 0.6183 (tpt) cc_final: 0.5782 (tpp) REVERT: H 32 CYS cc_start: 0.6995 (p) cc_final: 0.6743 (m) REVERT: Q 88 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6890 (tm-30) REVERT: Q 221 ASP cc_start: 0.7591 (t0) cc_final: 0.7060 (t70) REVERT: R 594 ARG cc_start: 0.6647 (ttp80) cc_final: 0.6399 (tmm160) REVERT: R 668 MET cc_start: 0.5850 (tpt) cc_final: 0.5309 (tpp) REVERT: S 94 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7125 (mmm-85) REVERT: T 69 THR cc_start: 0.8235 (p) cc_final: 0.7983 (p) REVERT: T 79 GLN cc_start: 0.7866 (mm110) cc_final: 0.7552 (mm110) REVERT: 6 91 TRP cc_start: 0.7023 (t-100) cc_final: 0.6439 (t-100) REVERT: 6 95 GLU cc_start: 0.7780 (tp30) cc_final: 0.7213 (tp30) REVERT: 6 257 LYS cc_start: 0.8010 (mttt) cc_final: 0.7765 (mtpt) REVERT: 6 485 GLU cc_start: 0.7873 (tp30) cc_final: 0.7526 (mm-30) REVERT: 7 668 MET cc_start: 0.6210 (tpt) cc_final: 0.5599 (tpp) REVERT: 8 13 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7451 (mmm160) REVERT: 8 64 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8074 (mmmt) REVERT: 9 69 THR cc_start: 0.8214 (p) cc_final: 0.7963 (p) outliers start: 34 outliers final: 28 residues processed: 264 average time/residue: 0.1545 time to fit residues: 66.0426 Evaluate side-chains 262 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 245 ASP 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 28 THR Chi-restraints excluded: chain H residue 48 ILE 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 108 CYS Chi-restraints excluded: chain Q residue 220 CYS 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 630 LEU Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 220 CYS Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 8 residue 28 THR Chi-restraints excluded: chain 8 residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 141 optimal weight: 7.9990 chunk 220 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 ASN H 77 GLN S 77 GLN S 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110618 restraints weight = 31107.313| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.76 r_work: 0.3079 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23580 Z= 0.133 Angle : 0.616 8.204 32343 Z= 0.308 Chirality : 0.042 0.280 3993 Planarity : 0.004 0.051 3801 Dihedral : 4.816 22.983 2826 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.04 % Favored : 93.50 % Rotamer: Outliers : 1.34 % Allowed : 15.54 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2583 helix: 2.02 (0.24), residues: 453 sheet: -0.13 (0.20), residues: 648 loop : -1.50 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 6 281 TYR 0.023 0.001 TYR L 91 PHE 0.016 0.002 PHE 6 346 TRP 0.027 0.001 TRP A 345 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (23376) covalent geometry : angle 0.59008 / 0.30 (31764) SS BOND : bond 0.00379 / 0.26 ( 33) SS BOND : angle 0.84055 / 0.55 ( 66) hydrogen bonds : bond 0.03835 / 2.61 ( 780) hydrogen bonds : angle 5.17006 / 3.54 ( 2007) link_ALPHA1-2 : bond 0.00290 / 0.16 ( 6) link_ALPHA1-2 : angle 1.48378 / 0.85 ( 18) link_ALPHA1-3 : bond 0.00631 / 0.41 ( 12) link_ALPHA1-3 : angle 1.47753 / 0.89 ( 36) link_ALPHA1-6 : bond 0.00344 / 0.22 ( 12) link_ALPHA1-6 : angle 1.44722 / 0.87 ( 36) link_BETA1-4 : bond 0.00436 / 0.27 ( 48) link_BETA1-4 : angle 1.22959 / 0.86 ( 144) link_BETA1-6 : bond 0.00516 / 0.30 ( 9) link_BETA1-6 : angle 1.10025 / 0.65 ( 27) link_NAG-ASN : bond 0.00292 / 0.17 ( 75) link_NAG-ASN : angle 1.76212 / 1.24 ( 225) link_TRANS : bond 0.00084 / 0.05 ( 9) link_TRANS : angle 0.42377 / 0.27 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5063.55 seconds wall clock time: 88 minutes 6.79 seconds (5286.79 seconds total)