Starting phenix.real_space_refine on Thu Mar 5 14:29:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2p_25621/03_2026/7t2p_25621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2p_25621/03_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_25621/03_2026/7t2p_25621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2p_25621/03_2026/7t2p_25621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t2p_25621/03_2026/7t2p_25621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2p_25621/03_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-5986/lib/python3.9/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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "R" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "7" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "8" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "9" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "7" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.99, per 1000 atoms: 0.22 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: 2.33 Conformation dependent library (CDL) restraints added in 913.0 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: 0.86 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: 4.00 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4393 1.32 - 1.47: 8428 1.47 - 1.61: 10345 1.61 - 1.76: 41 1.76 - 1.90: 169 Bond restraints: 23376 Sorted by residual: bond pdb=" NE1 TRP Q 290 " pdb=" CE2 TRP Q 290 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.47e+01 bond pdb=" NE1 TRP A 290 " pdb=" CE2 TRP A 290 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.10e-02 8.26e+03 3.45e+01 bond pdb=" NE1 TRP 6 290 " pdb=" CE2 TRP 6 290 " ideal model delta sigma weight residual 1.370 1.306 0.064 1.10e-02 8.26e+03 3.41e+01 bond pdb=" CB LEU R 674 " pdb=" CG LEU R 674 " ideal model delta sigma weight residual 1.530 1.641 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" CB LEU B 674 " pdb=" CG LEU B 674 " ideal model delta sigma weight residual 1.530 1.640 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 31653 7.12 - 14.24: 108 14.24 - 21.36: 0 21.36 - 28.48: 0 28.48 - 35.60: 3 Bond angle restraints: 31764 Sorted by residual: angle pdb=" C2 NAG A 610 " pdb=" N2 NAG A 610 " pdb=" C7 NAG A 610 " ideal model delta sigma weight residual 124.56 160.16 -35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG 6 610 " pdb=" N2 NAG 6 610 " pdb=" C7 NAG 6 610 " ideal model delta sigma weight residual 124.56 160.16 -35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C2 NAG Q 610 " pdb=" N2 NAG Q 610 " pdb=" C7 NAG Q 610 " ideal model delta sigma weight residual 124.56 160.14 -35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N VAL A 32 " pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 108.95 117.06 -8.11 9.80e-01 1.04e+00 6.84e+01 angle pdb=" N VAL Q 32 " pdb=" CA VAL Q 32 " pdb=" C VAL Q 32 " ideal model delta sigma weight residual 108.95 117.04 -8.09 9.80e-01 1.04e+00 6.81e+01 ... (remaining 31759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 15372 21.30 - 42.61: 447 42.61 - 63.91: 93 63.91 - 85.21: 84 85.21 - 106.51: 51 Dihedral angle restraints: 16047 sinusoidal: 8424 harmonic: 7623 Sorted by residual: dihedral pdb=" C PHE R 537 " pdb=" N PHE R 537 " pdb=" CA PHE R 537 " pdb=" CB PHE R 537 " ideal model delta harmonic sigma weight residual -122.60 -111.05 -11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE 7 537 " pdb=" N PHE 7 537 " pdb=" CA PHE 7 537 " pdb=" CB PHE 7 537 " ideal model delta harmonic sigma weight residual -122.60 -111.06 -11.54 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE B 537 " pdb=" N PHE B 537 " pdb=" CA PHE B 537 " pdb=" CB PHE B 537 " ideal model delta harmonic sigma weight residual -122.60 -111.07 -11.53 0 2.50e+00 1.60e-01 2.13e+01 ... (remaining 16044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2533 0.107 - 0.213: 858 0.213 - 0.320: 380 0.320 - 0.426: 144 0.426 - 0.533: 78 Chirality restraints: 3993 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 3990 not shown) Planarity restraints: 3885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.298 2.00e-02 2.50e+03 2.51e-01 7.86e+02 pdb=" C7 NAG A 602 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.186 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.430 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 602 " -0.298 2.00e-02 2.50e+03 2.51e-01 7.86e+02 pdb=" C7 NAG Q 602 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG Q 602 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG Q 602 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG Q 602 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 602 " -0.298 2.00e-02 2.50e+03 2.51e-01 7.85e+02 pdb=" C7 NAG 6 602 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG 6 602 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG 6 602 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG 6 602 " -0.022 2.00e-02 2.50e+03 ... (remaining 3882 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 7849 2.88 - 3.38: 20574 3.38 - 3.89: 38824 3.89 - 4.39: 45265 4.39 - 4.90: 72690 Nonbonded interactions: 185202 Sorted by model distance: nonbonded pdb=" OD1 ASP A 89 " pdb=" NZ LYS B 589 " model vdw 2.373 3.120 nonbonded pdb=" OD1 ASP Q 89 " pdb=" NZ LYS R 589 " model vdw 2.373 3.120 nonbonded pdb=" OD1 ASP 6 89 " pdb=" NZ LYS 7 589 " model vdw 2.373 3.120 nonbonded pdb=" NZ LYS A 254 " pdb=" OD2 ASP L 92 " model vdw 2.390 3.120 nonbonded pdb=" NZ LYS Q 254 " pdb=" OD2 ASP T 92 " model vdw 2.390 3.120 ... (remaining 185197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'J' selection = chain 'g' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain 'D' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'V' selection = chain 'b' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' } ncs_group { reference = (chain '3' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } ncs_group { reference = chain '6' selection = chain 'A' selection = chain 'Q' } ncs_group { reference = chain '7' selection = chain 'B' selection = chain 'R' } ncs_group { reference = chain '8' selection = chain 'H' selection = chain 'S' } ncs_group { reference = chain '9' selection = chain 'L' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'I' selection = chain 'Z' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.930 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.249 23580 Z= 1.217 Angle : 1.896 35.605 32343 Z= 1.182 Chirality : 0.152 0.533 3993 Planarity : 0.011 0.251 3801 Dihedral : 13.523 106.514 11013 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 1.39 % Allowed : 3.14 % Favored : 95.47 % Rotamer: Outliers : 0.39 % Allowed : 1.04 % Favored : 98.57 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.02258 (23376) covalent geometry : angle 1.85451 (31764) SS BOND : bond 0.07562 ( 33) SS BOND : angle 2.85578 ( 66) hydrogen bonds : bond 0.18789 ( 780) hydrogen bonds : angle 7.59337 ( 2007) link_ALPHA1-2 : bond 0.08532 ( 6) link_ALPHA1-2 : angle 4.13134 ( 18) link_ALPHA1-3 : bond 0.08691 ( 12) link_ALPHA1-3 : angle 4.47246 ( 36) link_ALPHA1-6 : bond 0.05477 ( 12) link_ALPHA1-6 : angle 3.74196 ( 36) link_BETA1-4 : bond 0.07212 ( 48) link_BETA1-4 : angle 4.44336 ( 144) link_BETA1-6 : bond 0.05504 ( 9) link_BETA1-6 : angle 2.93748 ( 27) link_NAG-ASN : bond 0.07841 ( 75) link_NAG-ASN : angle 2.82176 ( 225) link_TRANS : bond 0.00559 ( 9) link_TRANS : angle 1.58406 ( 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 : 0.785 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: 0.1685 time to fit residues: 130.9620 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 : 0.589 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 223 HIS ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 56 ASN H 77 GLN Q 223 HIS ** R 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 ASN S 77 GLN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 223 HIS ** 7 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 77 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107726 restraints weight = 30193.528| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.83 r_work: 0.3192 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23580 Z= 0.185 Angle : 0.843 12.371 32343 Z= 0.417 Chirality : 0.049 0.379 3993 Planarity : 0.005 0.053 3801 Dihedral : 11.302 84.847 6126 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.56 % Favored : 95.97 % Rotamer: Outliers : 1.56 % Allowed : 7.27 % Favored : 91.17 % 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: 1.30 (0.25), 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 0.019 0.002 TYR A 401 PHE 0.022 0.002 PHE R 537 TRP 0.030 0.002 TRP R 625 HIS 0.004 0.001 HIS Q 210 Details of bonding type rmsd covalent geometry : bond 0.00394 (23376) covalent geometry : angle 0.79196 (31764) SS BOND : bond 0.00309 ( 33) SS BOND : angle 0.77015 ( 66) hydrogen bonds : bond 0.06464 ( 780) hydrogen bonds : angle 6.13009 ( 2007) link_ALPHA1-2 : bond 0.00288 ( 6) link_ALPHA1-2 : angle 2.08324 ( 18) link_ALPHA1-3 : bond 0.01320 ( 12) link_ALPHA1-3 : angle 1.55460 ( 36) link_ALPHA1-6 : bond 0.00656 ( 12) link_ALPHA1-6 : angle 1.70702 ( 36) link_BETA1-4 : bond 0.00780 ( 48) link_BETA1-4 : angle 2.46396 ( 144) link_BETA1-6 : bond 0.00948 ( 9) link_BETA1-6 : angle 1.02888 ( 27) link_NAG-ASN : bond 0.00739 ( 75) link_NAG-ASN : angle 2.86269 ( 225) link_TRANS : bond 0.00150 ( 9) link_TRANS : angle 0.71472 ( 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 382 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 346 time to evaluate : 0.820 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: symmetry clash REVERT: A 257 LYS cc_start: 0.7639 (mttt) cc_final: 0.7439 (mtpt) REVERT: A 290 TRP cc_start: 0.8304 (m100) cc_final: 0.8095 (m100) REVERT: A 324 ILE cc_start: 0.8468 (pt) cc_final: 0.8265 (pt) REVERT: B 553 THR cc_start: 0.6260 (p) cc_final: 0.5736 (t) REVERT: B 563 ILE cc_start: 0.7604 (mt) cc_final: 0.7267 (tp) REVERT: B 641 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7330 (mp0) REVERT: B 668 MET cc_start: 0.6225 (tpt) cc_final: 0.5901 (tpp) REVERT: H 6 GLU cc_start: 0.5841 (mp0) cc_final: 0.5511 (mp0) REVERT: H 21 THR cc_start: 0.7785 (m) cc_final: 0.7525 (p) REVERT: H 55 ASP cc_start: 0.8048 (m-30) cc_final: 0.7766 (m-30) REVERT: L 91 TYR cc_start: 0.8145 (p90) cc_final: 0.7677 (p90) REVERT: Q 88 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7255 (tm-30) REVERT: Q 95 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7653 (tp30) REVERT: Q 172 MET cc_start: 0.8428 (tpp) cc_final: 0.8194 (tpt) REVERT: R 553 THR cc_start: 0.6430 (p) cc_final: 0.5088 (t) REVERT: R 557 ARG cc_start: 0.6134 (mtm110) cc_final: 0.5798 (ttp80) REVERT: R 590 ASN cc_start: 0.5117 (m-40) cc_final: 0.4814 (m-40) REVERT: R 631 ILE cc_start: 0.7988 (tp) cc_final: 0.7696 (mt) REVERT: R 641 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7389 (mp0) REVERT: S 5 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8136 (tp-100) REVERT: S 32 CYS cc_start: 0.6813 (t) cc_final: 0.6613 (p) REVERT: 6 95 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7594 (tp30) REVERT: 6 257 LYS cc_start: 0.8083 (mttt) cc_final: 0.7712 (mtpt) REVERT: 6 281 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8125 (mtp-110) REVERT: 6 325 MET cc_start: 0.8377 (mtm) cc_final: 0.8116 (mtp) REVERT: 7 553 THR cc_start: 0.6763 (p) cc_final: 0.6287 (t) REVERT: 7 625 TRP cc_start: 0.7293 (t-100) cc_final: 0.6679 (t-100) REVERT: 7 667 ASN cc_start: 0.6921 (m-40) cc_final: 0.6514 (t0) REVERT: 7 668 MET cc_start: 0.6273 (tpt) cc_final: 0.5564 (tpp) REVERT: 8 6 GLU cc_start: 0.5659 (mp0) cc_final: 0.5358 (mp0) REVERT: 8 69 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6859 (mt) REVERT: 9 104 LEU cc_start: 0.5925 (tp) cc_final: 0.5530 (tp) outliers start: 36 outliers final: 23 residues processed: 374 average time/residue: 0.1591 time to fit residues: 93.0305 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 : 0.764 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN 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 = 0.3874 r_free = 0.3874 target = 0.148085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108369 restraints weight = 31046.164| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.69 r_work: 0.3069 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23580 Z= 0.193 Angle : 0.754 13.272 32343 Z= 0.371 Chirality : 0.048 0.324 3993 Planarity : 0.005 0.044 3801 Dihedral : 9.725 76.100 6114 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.76 % Favored : 94.77 % Rotamer: Outliers : 2.03 % Allowed : 9.35 % Favored : 88.61 % 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: -0.49 (0.16), residues: 2583 helix: 1.06 (0.23), residues: 453 sheet: 0.12 (0.19), residues: 684 loop : -1.01 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 594 TYR 0.027 0.002 TYR 6 401 PHE 0.022 0.003 PHE R 537 TRP 0.028 0.002 TRP 6 91 HIS 0.003 0.001 HIS Q 364 Details of bonding type rmsd covalent geometry : bond 0.00447 (23376) covalent geometry : angle 0.71461 (31764) SS BOND : bond 0.00564 ( 33) SS BOND : angle 0.90662 ( 66) hydrogen bonds : bond 0.05206 ( 780) hydrogen bonds : angle 5.73212 ( 2007) link_ALPHA1-2 : bond 0.00335 ( 6) link_ALPHA1-2 : angle 1.68878 ( 18) link_ALPHA1-3 : bond 0.01273 ( 12) link_ALPHA1-3 : angle 1.54630 ( 36) link_ALPHA1-6 : bond 0.00789 ( 12) link_ALPHA1-6 : angle 1.67769 ( 36) link_BETA1-4 : bond 0.00624 ( 48) link_BETA1-4 : angle 1.91974 ( 144) link_BETA1-6 : bond 0.00663 ( 9) link_BETA1-6 : angle 1.10408 ( 27) link_NAG-ASN : bond 0.00496 ( 75) link_NAG-ASN : angle 2.41155 ( 225) link_TRANS : bond 0.00122 ( 9) link_TRANS : angle 0.50076 ( 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 332 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.8470 (tpp) cc_final: 0.8128 (tpt) REVERT: A 257 LYS cc_start: 0.7722 (mttt) cc_final: 0.7466 (mtpt) REVERT: A 290 TRP cc_start: 0.8322 (m100) cc_final: 0.8014 (m100) REVERT: A 309 MET cc_start: 0.8314 (ttp) cc_final: 0.8036 (ttt) REVERT: A 404 MET cc_start: 0.8269 (mtp) cc_final: 0.7790 (mmm) REVERT: A 501 GLU cc_start: 0.7922 (tt0) cc_final: 0.7608 (tt0) REVERT: B 553 THR cc_start: 0.5982 (p) cc_final: 0.5652 (t) REVERT: B 633 LYS cc_start: 0.7033 (mmtm) cc_final: 0.6801 (mmtm) REVERT: B 641 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7149 (mp0) REVERT: B 668 MET cc_start: 0.6135 (tpt) cc_final: 0.5866 (tpp) REVERT: H 6 GLU cc_start: 0.5992 (mp0) cc_final: 0.5765 (mp0) REVERT: H 55 ASP cc_start: 0.8235 (m-30) cc_final: 0.7993 (m-30) REVERT: L 91 TYR cc_start: 0.8132 (p90) cc_final: 0.7687 (p90) REVERT: Q 88 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6883 (tm-30) REVERT: Q 95 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7556 (tp30) REVERT: Q 172 MET cc_start: 0.8482 (tpp) cc_final: 0.8269 (tpt) REVERT: Q 309 MET cc_start: 0.8589 (ttt) cc_final: 0.8210 (ttt) REVERT: R 590 ASN cc_start: 0.4369 (m-40) cc_final: 0.4027 (t0) REVERT: R 599 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7766 (mm-30) REVERT: R 631 ILE cc_start: 0.8232 (tp) cc_final: 0.7950 (mt) REVERT: R 668 MET cc_start: 0.5688 (tpt) cc_final: 0.5184 (tpp) REVERT: S 13 ARG cc_start: 0.8304 (mpt180) cc_final: 0.8049 (tpp80) REVERT: S 55 ASP cc_start: 0.8168 (m-30) cc_final: 0.7864 (m-30) REVERT: T 33 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8606 (tp) REVERT: 6 103 LYS cc_start: 0.8592 (mttt) cc_final: 0.8375 (mttp) REVERT: 6 257 LYS cc_start: 0.8068 (mttt) cc_final: 0.7703 (mtpt) REVERT: 6 290 TRP cc_start: 0.8379 (m100) cc_final: 0.7934 (m100) REVERT: 6 309 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8172 (ttt) REVERT: 7 553 THR cc_start: 0.6450 (p) cc_final: 0.5968 (t) REVERT: 7 667 ASN cc_start: 0.7043 (m-40) cc_final: 0.6638 (t0) REVERT: 7 668 MET cc_start: 0.6288 (tpt) cc_final: 0.5441 (tpp) REVERT: 9 104 LEU cc_start: 0.6126 (tp) cc_final: 0.5460 (tt) outliers start: 47 outliers final: 31 residues processed: 317 average time/residue: 0.1621 time to fit residues: 79.5012 Evaluate side-chains 278 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 3 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 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 33 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 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 7 residue 641 GLU 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: 0.0030 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 635 ASN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 82AASN S 105 GLN 7 640 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107930 restraints weight = 31043.467| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.82 r_work: 0.3051 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 23580 Z= 0.183 Angle : 0.715 10.167 32343 Z= 0.352 Chirality : 0.046 0.322 3993 Planarity : 0.005 0.052 3801 Dihedral : 9.097 70.862 6112 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.96 % Favored : 94.62 % Rotamer: Outliers : 2.38 % Allowed : 9.91 % Favored : 87.71 % 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 (0.16), residues: 2583 helix: 1.41 (0.24), residues: 453 sheet: 0.01 (0.19), residues: 663 loop : -1.15 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 7 594 TYR 0.024 0.002 TYR 6 401 PHE 0.018 0.002 PHE R 537 TRP 0.026 0.001 TRP 6 91 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd covalent geometry : bond 0.00432 (23376) covalent geometry : angle 0.67386 (31764) SS BOND : bond 0.00348 ( 33) SS BOND : angle 1.25424 ( 66) hydrogen bonds : bond 0.04706 ( 780) hydrogen bonds : angle 5.55687 ( 2007) link_ALPHA1-2 : bond 0.00217 ( 6) link_ALPHA1-2 : angle 1.68367 ( 18) link_ALPHA1-3 : bond 0.01149 ( 12) link_ALPHA1-3 : angle 1.70619 ( 36) link_ALPHA1-6 : bond 0.00780 ( 12) link_ALPHA1-6 : angle 1.85306 ( 36) link_BETA1-4 : bond 0.00517 ( 48) link_BETA1-4 : angle 1.74526 ( 144) link_BETA1-6 : bond 0.00643 ( 9) link_BETA1-6 : angle 1.09022 ( 27) link_NAG-ASN : bond 0.00391 ( 75) link_NAG-ASN : angle 2.35851 ( 225) link_TRANS : bond 0.00130 ( 9) link_TRANS : angle 0.46858 ( 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 330 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 0.907 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 88 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 92 GLN cc_start: 0.8260 (tp40) cc_final: 0.7900 (tp40) REVERT: A 95 GLU cc_start: 0.8110 (tp30) cc_final: 0.7720 (tp30) REVERT: A 290 TRP cc_start: 0.8340 (m100) cc_final: 0.7978 (m100) REVERT: A 309 MET cc_start: 0.8363 (ttp) cc_final: 0.8149 (ttt) REVERT: A 404 MET cc_start: 0.8301 (mtp) cc_final: 0.8097 (mmm) REVERT: A 501 GLU cc_start: 0.8005 (tt0) cc_final: 0.7732 (tt0) REVERT: B 553 THR cc_start: 0.5819 (p) cc_final: 0.5535 (t) REVERT: B 599 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: B 633 LYS cc_start: 0.6975 (mmtm) cc_final: 0.6775 (mmtm) REVERT: B 635 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7358 (p0) REVERT: B 668 MET cc_start: 0.6168 (tpt) cc_final: 0.5677 (tpt) REVERT: H 6 GLU cc_start: 0.5985 (mp0) cc_final: 0.5667 (mp0) REVERT: H 32 CYS cc_start: 0.7034 (p) cc_final: 0.6568 (m) REVERT: L 91 TYR cc_start: 0.8142 (p90) cc_final: 0.7653 (p90) REVERT: Q 88 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6898 (tm-30) REVERT: Q 95 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7548 (tp30) REVERT: Q 290 TRP cc_start: 0.8397 (m100) cc_final: 0.8052 (m100) REVERT: Q 309 MET cc_start: 0.8527 (ttt) cc_final: 0.8187 (ttt) REVERT: Q 497 TYR cc_start: 0.9017 (m-80) cc_final: 0.8708 (m-80) REVERT: R 590 ASN cc_start: 0.4219 (m-40) cc_final: 0.3975 (t0) REVERT: R 631 ILE cc_start: 0.8129 (tp) cc_final: 0.7893 (mt) REVERT: R 668 MET cc_start: 0.5787 (tpt) cc_final: 0.5212 (tpp) REVERT: S 13 ARG cc_start: 0.8240 (mpt180) cc_final: 0.8036 (tpp-160) REVERT: S 46 GLU cc_start: 0.7785 (tt0) cc_final: 0.7407 (pt0) REVERT: S 55 ASP cc_start: 0.8269 (m-30) cc_final: 0.8007 (m-30) REVERT: S 94 ARG cc_start: 0.7203 (mmm-85) cc_final: 0.6974 (mmm-85) REVERT: 6 91 TRP cc_start: 0.6848 (t-100) cc_final: 0.6175 (t-100) REVERT: 6 95 GLU cc_start: 0.7585 (tp30) cc_final: 0.6885 (tp30) REVERT: 6 103 LYS cc_start: 0.8830 (mttt) cc_final: 0.8602 (mttp) REVERT: 6 221 ASP cc_start: 0.8289 (t0) cc_final: 0.7932 (t0) REVERT: 6 257 LYS cc_start: 0.8053 (mttt) cc_final: 0.7676 (mtpt) REVERT: 6 290 TRP cc_start: 0.8394 (m100) cc_final: 0.8055 (m100) REVERT: 7 667 ASN cc_start: 0.6956 (m-40) cc_final: 0.6575 (t0) REVERT: 7 668 MET cc_start: 0.6218 (tpt) cc_final: 0.5699 (tpp) REVERT: 8 32 CYS cc_start: 0.7092 (p) cc_final: 0.6780 (m) REVERT: 8 94 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.7322 (mmm-85) REVERT: 9 42 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8344 (pttm) REVERT: 9 104 LEU cc_start: 0.6090 (tp) cc_final: 0.5415 (tt) outliers start: 55 outliers final: 40 residues processed: 316 average time/residue: 0.1520 time to fit residues: 75.8459 Evaluate side-chains 283 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 596 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 635 ASN 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 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 3 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS Chi-restraints excluded: chain 6 residue 245 ASP Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 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: 2.9990 chunk 160 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100NHIS ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 82AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.181938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.145212 restraints weight = 31546.154| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.28 r_work: 0.3571 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23580 Z= 0.163 Angle : 0.681 8.139 32343 Z= 0.335 Chirality : 0.045 0.307 3993 Planarity : 0.004 0.041 3801 Dihedral : 8.714 67.574 6112 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.30 % Favored : 94.19 % Rotamer: Outliers : 2.38 % Allowed : 10.82 % Favored : 86.80 % 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: -0.52 (0.17), residues: 2583 helix: 1.63 (0.24), residues: 453 sheet: 0.01 (0.19), residues: 681 loop : -1.20 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 8 13 TYR 0.022 0.001 TYR 6 401 PHE 0.018 0.002 PHE R 537 TRP 0.018 0.001 TRP 6 91 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00381 (23376) covalent geometry : angle 0.64052 (31764) SS BOND : bond 0.00361 ( 33) SS BOND : angle 1.62701 ( 66) hydrogen bonds : bond 0.04423 ( 780) hydrogen bonds : angle 5.44803 ( 2007) link_ALPHA1-2 : bond 0.00257 ( 6) link_ALPHA1-2 : angle 1.61560 ( 18) link_ALPHA1-3 : bond 0.01107 ( 12) link_ALPHA1-3 : angle 1.65841 ( 36) link_ALPHA1-6 : bond 0.00808 ( 12) link_ALPHA1-6 : angle 1.83393 ( 36) link_BETA1-4 : bond 0.00506 ( 48) link_BETA1-4 : angle 1.58532 ( 144) link_BETA1-6 : bond 0.00625 ( 9) link_BETA1-6 : angle 1.10261 ( 27) link_NAG-ASN : bond 0.00380 ( 75) link_NAG-ASN : angle 2.22192 ( 225) link_TRANS : bond 0.00109 ( 9) link_TRANS : angle 0.43144 ( 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 324 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.656 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 92 GLN cc_start: 0.8646 (tp40) cc_final: 0.8185 (tp40) REVERT: A 95 GLU cc_start: 0.8258 (tp30) cc_final: 0.7982 (tp30) REVERT: A 290 TRP cc_start: 0.8359 (m100) cc_final: 0.8149 (m100) REVERT: A 501 GLU cc_start: 0.8092 (tt0) cc_final: 0.7881 (tt0) REVERT: B 553 THR cc_start: 0.5804 (p) cc_final: 0.5496 (t) REVERT: B 599 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: B 635 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7895 (p0) REVERT: B 668 MET cc_start: 0.6196 (tpt) cc_final: 0.5634 (tpt) REVERT: H 6 GLU cc_start: 0.5998 (mp0) cc_final: 0.5725 (mp0) REVERT: H 32 CYS cc_start: 0.7090 (p) cc_final: 0.6706 (m) REVERT: H 75 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8424 (pttp) REVERT: L 91 TYR cc_start: 0.8197 (p90) cc_final: 0.7967 (p90) REVERT: Q 88 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7448 (tm-30) REVERT: Q 290 TRP cc_start: 0.8401 (m100) cc_final: 0.8200 (m100) REVERT: Q 309 MET cc_start: 0.8376 (ttt) cc_final: 0.8120 (ttt) REVERT: Q 497 TYR cc_start: 0.8950 (m-80) cc_final: 0.8652 (m-80) REVERT: R 590 ASN cc_start: 0.4524 (m-40) cc_final: 0.4208 (t0) REVERT: R 668 MET cc_start: 0.5650 (tpt) cc_final: 0.5056 (tpp) REVERT: S 32 CYS cc_start: 0.6991 (p) cc_final: 0.6680 (m) REVERT: S 46 GLU cc_start: 0.7863 (tt0) cc_final: 0.7615 (pt0) REVERT: S 55 ASP cc_start: 0.8143 (m-30) cc_final: 0.7899 (m-30) REVERT: 6 91 TRP cc_start: 0.7152 (t-100) cc_final: 0.6686 (t-100) REVERT: 6 95 GLU cc_start: 0.7914 (tp30) cc_final: 0.7357 (tp30) REVERT: 6 221 ASP cc_start: 0.7884 (t0) cc_final: 0.7630 (t0) REVERT: 6 290 TRP cc_start: 0.8391 (m100) cc_final: 0.8184 (m100) REVERT: 7 545 MET cc_start: 0.7144 (mtp) cc_final: 0.6543 (mtp) REVERT: 7 667 ASN cc_start: 0.6970 (m-40) cc_final: 0.6584 (t0) REVERT: 7 668 MET cc_start: 0.6412 (tpt) cc_final: 0.5858 (tpp) REVERT: 8 28 THR cc_start: 0.8237 (p) cc_final: 0.8032 (m) outliers start: 55 outliers final: 45 residues processed: 310 average time/residue: 0.1470 time to fit residues: 71.8018 Evaluate side-chains 289 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 B residue 635 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 R residue 595 VAL Chi-restraints excluded: chain T residue 3 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 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 220 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 306 ASN Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 476 ASN Chi-restraints excluded: chain 7 residue 595 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 64 optimal weight: 5.9990 chunk 236 optimal weight: 0.0670 chunk 144 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 39 optimal weight: 0.0050 chunk 225 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 77 GLN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 82AASN S 100NHIS T 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.181074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.146427 restraints weight = 31736.330| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.05 r_work: 0.3552 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23580 Z= 0.164 Angle : 0.672 9.066 32343 Z= 0.330 Chirality : 0.045 0.303 3993 Planarity : 0.004 0.052 3801 Dihedral : 8.431 64.329 6112 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.38 % Favored : 94.08 % Rotamer: Outliers : 2.21 % Allowed : 12.21 % Favored : 85.58 % 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: -0.58 (0.17), residues: 2583 helix: 1.73 (0.24), residues: 453 sheet: -0.09 (0.19), residues: 687 loop : -1.27 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 13 TYR 0.036 0.001 TYR T 91 PHE 0.016 0.002 PHE R 537 TRP 0.016 0.001 TRP 6 91 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd covalent geometry : bond 0.00384 (23376) covalent geometry : angle 0.63573 (31764) SS BOND : bond 0.00508 ( 33) SS BOND : angle 1.26661 ( 66) hydrogen bonds : bond 0.04322 ( 780) hydrogen bonds : angle 5.36732 ( 2007) link_ALPHA1-2 : bond 0.00277 ( 6) link_ALPHA1-2 : angle 1.59465 ( 18) link_ALPHA1-3 : bond 0.01135 ( 12) link_ALPHA1-3 : angle 1.70560 ( 36) link_ALPHA1-6 : bond 0.00822 ( 12) link_ALPHA1-6 : angle 1.84845 ( 36) link_BETA1-4 : bond 0.00497 ( 48) link_BETA1-4 : angle 1.47750 ( 144) link_BETA1-6 : bond 0.00602 ( 9) link_BETA1-6 : angle 1.10701 ( 27) link_NAG-ASN : bond 0.00353 ( 75) link_NAG-ASN : angle 2.13613 ( 225) link_TRANS : bond 0.00114 ( 9) link_TRANS : angle 0.41202 ( 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 314 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 92 GLN cc_start: 0.8656 (tp40) cc_final: 0.8154 (tp40) REVERT: A 95 GLU cc_start: 0.8213 (tp30) cc_final: 0.7745 (tp30) REVERT: B 599 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: B 668 MET cc_start: 0.6370 (tpt) cc_final: 0.6125 (tpt) REVERT: H 32 CYS cc_start: 0.7037 (p) cc_final: 0.6699 (m) REVERT: Q 88 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7472 (tm-30) REVERT: Q 91 TRP cc_start: 0.7461 (t-100) cc_final: 0.7231 (t-100) REVERT: Q 309 MET cc_start: 0.8367 (ttt) cc_final: 0.8124 (ttt) REVERT: Q 497 TYR cc_start: 0.8944 (m-80) cc_final: 0.8650 (m-80) REVERT: R 590 ASN cc_start: 0.4651 (m-40) cc_final: 0.4315 (t0) REVERT: R 668 MET cc_start: 0.5614 (tpt) cc_final: 0.5024 (tpp) REVERT: S 32 CYS cc_start: 0.7054 (p) cc_final: 0.6818 (m) REVERT: S 55 ASP cc_start: 0.8129 (m-30) cc_final: 0.7891 (m-30) REVERT: 6 91 TRP cc_start: 0.7212 (t-100) cc_final: 0.6742 (t-100) REVERT: 6 95 GLU cc_start: 0.7962 (tp30) cc_final: 0.7446 (tp30) REVERT: 6 221 ASP cc_start: 0.7927 (t0) cc_final: 0.7645 (t0) REVERT: 7 545 MET cc_start: 0.7194 (mtp) cc_final: 0.6957 (mtp) REVERT: 7 668 MET cc_start: 0.6486 (tpt) cc_final: 0.5837 (tpp) REVERT: 8 28 THR cc_start: 0.8451 (p) cc_final: 0.8192 (m) REVERT: 9 79 GLN cc_start: 0.8035 (mm110) cc_final: 0.7777 (mm110) outliers start: 51 outliers final: 41 residues processed: 299 average time/residue: 0.1477 time to fit residues: 70.6751 Evaluate side-chains 271 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 203 GLU Chi-restraints excluded: chain A residue 318 THR 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 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 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 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 476 ASN Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain 6 residue 40 ILE Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 67 MET Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 108 CYS 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 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: 3.9990 chunk 222 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 82AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.165616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.127474 restraints weight = 32041.196| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.66 r_work: 0.3310 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 23580 Z= 0.179 Angle : 0.675 8.816 32343 Z= 0.332 Chirality : 0.045 0.298 3993 Planarity : 0.004 0.049 3801 Dihedral : 8.265 61.867 6108 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.00 % Favored : 93.46 % Rotamer: Outliers : 2.42 % Allowed : 12.64 % 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: -0.68 (0.17), residues: 2583 helix: 1.86 (0.24), residues: 453 sheet: -0.16 (0.19), residues: 705 loop : -1.41 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 594 TYR 0.028 0.002 TYR T 91 PHE 0.016 0.002 PHE B 537 TRP 0.015 0.001 TRP 6 91 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd covalent geometry : bond 0.00426 (23376) covalent geometry : angle 0.64043 (31764) SS BOND : bond 0.00489 ( 33) SS BOND : angle 1.27246 ( 66) hydrogen bonds : bond 0.04336 ( 780) hydrogen bonds : angle 5.34833 ( 2007) link_ALPHA1-2 : bond 0.00278 ( 6) link_ALPHA1-2 : angle 1.57703 ( 18) link_ALPHA1-3 : bond 0.01144 ( 12) link_ALPHA1-3 : angle 1.75360 ( 36) link_ALPHA1-6 : bond 0.00806 ( 12) link_ALPHA1-6 : angle 1.83788 ( 36) link_BETA1-4 : bond 0.00485 ( 48) link_BETA1-4 : angle 1.41850 ( 144) link_BETA1-6 : bond 0.00563 ( 9) link_BETA1-6 : angle 1.12288 ( 27) link_NAG-ASN : bond 0.00345 ( 75) link_NAG-ASN : angle 2.09709 ( 225) link_TRANS : bond 0.00127 ( 9) link_TRANS : angle 0.42113 ( 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 298 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 92 GLN cc_start: 0.8551 (tp40) cc_final: 0.8121 (tp40) REVERT: A 95 GLU cc_start: 0.8074 (tp30) cc_final: 0.7626 (tp30) REVERT: A 333 GLN cc_start: 0.8397 (tt0) cc_final: 0.8185 (pt0) REVERT: B 599 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8142 (mm-30) REVERT: B 668 MET cc_start: 0.6325 (tpt) cc_final: 0.5710 (tpp) REVERT: H 28 THR cc_start: 0.8670 (p) cc_final: 0.8400 (m) REVERT: H 32 CYS cc_start: 0.7079 (p) cc_final: 0.6715 (m) REVERT: H 81 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7595 (ttmm) REVERT: Q 88 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7429 (tm-30) REVERT: Q 91 TRP cc_start: 0.7346 (t-100) cc_final: 0.7141 (t-100) REVERT: Q 497 TYR cc_start: 0.8996 (m-80) cc_final: 0.8718 (m-80) REVERT: R 590 ASN cc_start: 0.4573 (m-40) cc_final: 0.4276 (t0) REVERT: R 668 MET cc_start: 0.5637 (tpt) cc_final: 0.5067 (tpp) REVERT: S 28 THR cc_start: 0.8620 (p) cc_final: 0.8283 (m) REVERT: S 32 CYS cc_start: 0.7069 (p) cc_final: 0.6778 (m) REVERT: S 55 ASP cc_start: 0.8273 (m-30) cc_final: 0.8025 (m-30) REVERT: T 69 THR cc_start: 0.8109 (p) cc_final: 0.7860 (p) REVERT: 6 91 TRP cc_start: 0.7177 (t-100) cc_final: 0.6664 (t-100) REVERT: 6 95 GLU cc_start: 0.7908 (tp30) cc_final: 0.7319 (tp30) REVERT: 6 221 ASP cc_start: 0.8073 (t0) cc_final: 0.7737 (t70) REVERT: 7 545 MET cc_start: 0.7126 (mtp) cc_final: 0.6888 (mtp) REVERT: 7 668 MET cc_start: 0.6547 (tpt) cc_final: 0.5941 (tpp) REVERT: 8 28 THR cc_start: 0.8621 (p) cc_final: 0.8418 (m) REVERT: 9 79 GLN cc_start: 0.7973 (mm110) cc_final: 0.7697 (mm110) outliers start: 56 outliers final: 42 residues processed: 283 average time/residue: 0.1438 time to fit residues: 65.3298 Evaluate side-chains 272 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 203 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 108 CYS Chi-restraints excluded: chain Q residue 318 THR Chi-restraints excluded: chain Q residue 345 TRP Chi-restraints excluded: chain Q residue 368 THR Chi-restraints excluded: chain R residue 595 VAL Chi-restraints excluded: chain S residue 100 ASN 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 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 220 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 297 THR 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 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 5 THR Chi-restraints excluded: chain 9 residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 98 optimal weight: 0.0770 chunk 175 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN H 77 GLN L 79 GLN Q 336 ASN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 82AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.168411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129619 restraints weight = 31893.221| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.95 r_work: 0.3363 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23580 Z= 0.129 Angle : 0.626 7.935 32343 Z= 0.308 Chirality : 0.043 0.289 3993 Planarity : 0.004 0.051 3801 Dihedral : 7.900 59.913 6108 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.27 % Favored : 94.19 % Rotamer: Outliers : 2.08 % Allowed : 13.16 % Favored : 84.76 % 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: -0.56 (0.17), residues: 2583 helix: 1.98 (0.24), residues: 453 sheet: -0.12 (0.19), residues: 687 loop : -1.32 (0.17), residues: 1443 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 0.015 0.002 PHE R 537 TRP 0.015 0.001 TRP 6 91 HIS 0.002 0.001 HIS 6 364 Details of bonding type rmsd covalent geometry : bond 0.00289 (23376) covalent geometry : angle 0.59453 (31764) SS BOND : bond 0.00326 ( 33) SS BOND : angle 0.85626 ( 66) hydrogen bonds : bond 0.03940 ( 780) hydrogen bonds : angle 5.19219 ( 2007) link_ALPHA1-2 : bond 0.00370 ( 6) link_ALPHA1-2 : angle 1.52668 ( 18) link_ALPHA1-3 : bond 0.01190 ( 12) link_ALPHA1-3 : angle 1.72226 ( 36) link_ALPHA1-6 : bond 0.00885 ( 12) link_ALPHA1-6 : angle 1.81586 ( 36) link_BETA1-4 : bond 0.00500 ( 48) link_BETA1-4 : angle 1.30944 ( 144) link_BETA1-6 : bond 0.00604 ( 9) link_BETA1-6 : angle 1.11390 ( 27) link_NAG-ASN : bond 0.00325 ( 75) link_NAG-ASN : angle 1.95776 ( 225) link_TRANS : bond 0.00076 ( 9) link_TRANS : angle 0.40917 ( 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 296 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7996 (tp30) cc_final: 0.7499 (tp30) REVERT: A 203 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: B 609 ASN cc_start: 0.7250 (m-40) cc_final: 0.7020 (m-40) REVERT: B 668 MET cc_start: 0.6367 (tpt) cc_final: 0.5744 (tpp) REVERT: H 13 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7914 (mmt180) REVERT: H 32 CYS cc_start: 0.7023 (p) cc_final: 0.6633 (m) REVERT: H 46 GLU cc_start: 0.7947 (tt0) cc_final: 0.7537 (pt0) REVERT: H 94 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7298 (mtm-85) REVERT: Q 221 ASP cc_start: 0.7608 (t0) cc_final: 0.7133 (t70) REVERT: R 590 ASN cc_start: 0.4532 (m-40) cc_final: 0.4263 (t0) REVERT: R 668 MET cc_start: 0.5733 (tpt) cc_final: 0.5227 (tpp) REVERT: S 32 CYS cc_start: 0.7113 (p) cc_final: 0.6878 (m) REVERT: S 55 ASP cc_start: 0.8279 (m-30) cc_final: 0.7999 (m-30) REVERT: T 69 THR cc_start: 0.8110 (p) cc_final: 0.7868 (p) REVERT: 6 91 TRP cc_start: 0.7129 (t-100) cc_final: 0.6681 (t-100) REVERT: 6 95 GLU cc_start: 0.7867 (tp30) cc_final: 0.7240 (tp30) REVERT: 7 668 MET cc_start: 0.6509 (tpt) cc_final: 0.5868 (tpp) REVERT: 8 64 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8138 (mmmt) REVERT: 9 79 GLN cc_start: 0.7997 (mm110) cc_final: 0.7776 (mm110) outliers start: 48 outliers final: 36 residues processed: 283 average time/residue: 0.1508 time to fit residues: 68.2037 Evaluate side-chains 268 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 368 THR Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain 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 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 R residue 595 VAL Chi-restraints excluded: chain S residue 48 ILE 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 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 220 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 268 GLU 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 3 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 3 optimal weight: 10.0000 chunk 241 optimal weight: 0.0270 chunk 243 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 80 optimal weight: 0.0770 chunk 202 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 77 GLN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 ASN S 77 GLN S 82AASN S 105 GLN 8 100NHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131745 restraints weight = 32378.981| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.76 r_work: 0.3366 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23580 Z= 0.121 Angle : 0.621 9.062 32343 Z= 0.303 Chirality : 0.043 0.301 3993 Planarity : 0.004 0.050 3801 Dihedral : 7.582 59.777 6108 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.57 % Favored : 93.88 % Rotamer: Outliers : 1.47 % Allowed : 14.24 % Favored : 84.29 % 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: -0.54 (0.17), residues: 2583 helix: 2.04 (0.24), residues: 453 sheet: -0.08 (0.19), residues: 723 loop : -1.36 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 594 TYR 0.018 0.001 TYR 9 91 PHE 0.014 0.002 PHE R 537 TRP 0.019 0.001 TRP A 345 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00268 (23376) covalent geometry : angle 0.58929 (31764) SS BOND : bond 0.00330 ( 33) SS BOND : angle 0.87341 ( 66) hydrogen bonds : bond 0.03829 ( 780) hydrogen bonds : angle 5.07798 ( 2007) link_ALPHA1-2 : bond 0.00408 ( 6) link_ALPHA1-2 : angle 1.49612 ( 18) link_ALPHA1-3 : bond 0.01185 ( 12) link_ALPHA1-3 : angle 1.74396 ( 36) link_ALPHA1-6 : bond 0.00902 ( 12) link_ALPHA1-6 : angle 1.75233 ( 36) link_BETA1-4 : bond 0.00507 ( 48) link_BETA1-4 : angle 1.28606 ( 144) link_BETA1-6 : bond 0.00644 ( 9) link_BETA1-6 : angle 1.09606 ( 27) link_NAG-ASN : bond 0.00313 ( 75) link_NAG-ASN : angle 1.95827 ( 225) link_TRANS : bond 0.00074 ( 9) link_TRANS : angle 0.39532 ( 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 283 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7870 (tp30) cc_final: 0.7390 (tp30) REVERT: A 172 MET cc_start: 0.8306 (tpp) cc_final: 0.7499 (tpt) REVERT: A 290 TRP cc_start: 0.8451 (m100) cc_final: 0.8031 (m100) REVERT: A 485 GLU cc_start: 0.7883 (tp30) cc_final: 0.7568 (mm-30) REVERT: B 609 ASN cc_start: 0.7186 (m-40) cc_final: 0.6948 (m-40) REVERT: B 668 MET cc_start: 0.6353 (tpt) cc_final: 0.5722 (tpp) REVERT: H 32 CYS cc_start: 0.6967 (p) cc_final: 0.6662 (m) REVERT: H 46 GLU cc_start: 0.7931 (tt0) cc_final: 0.7598 (pt0) REVERT: H 94 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7357 (mtm-85) REVERT: Q 221 ASP cc_start: 0.7556 (t0) cc_final: 0.7103 (t70) REVERT: Q 290 TRP cc_start: 0.8415 (m100) cc_final: 0.8183 (m100) REVERT: R 590 ASN cc_start: 0.4501 (m-40) cc_final: 0.4258 (t0) REVERT: R 668 MET cc_start: 0.5720 (tpt) cc_final: 0.5227 (tpp) REVERT: T 69 THR cc_start: 0.8114 (p) cc_final: 0.7860 (p) REVERT: T 79 GLN cc_start: 0.8041 (mm110) cc_final: 0.7777 (mm110) REVERT: 6 91 TRP cc_start: 0.7144 (t-100) cc_final: 0.6721 (t-100) REVERT: 6 95 GLU cc_start: 0.7906 (tp30) cc_final: 0.7336 (tp30) REVERT: 7 667 ASN cc_start: 0.6912 (m-40) cc_final: 0.6511 (t0) REVERT: 7 668 MET cc_start: 0.6169 (tpt) cc_final: 0.5664 (tpp) REVERT: 8 13 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7357 (mmm160) REVERT: 8 64 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8077 (mmmt) REVERT: 9 79 GLN cc_start: 0.7989 (mm110) cc_final: 0.7781 (mm110) outliers start: 34 outliers final: 28 residues processed: 276 average time/residue: 0.1452 time to fit residues: 64.4362 Evaluate side-chains 257 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 268 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain 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 220 CYS 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 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 220 CYS Chi-restraints excluded: chain 6 residue 262 SER Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 7 residue 595 VAL 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: 0.9990 chunk 93 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN H 77 GLN ** R 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 672 GLN S 56 ASN S 77 GLN S 82AASN S 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.167547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129290 restraints weight = 32026.200| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.91 r_work: 0.3338 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23580 Z= 0.152 Angle : 0.647 8.997 32343 Z= 0.316 Chirality : 0.044 0.287 3993 Planarity : 0.004 0.056 3801 Dihedral : 7.532 59.967 6108 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.96 % Favored : 93.53 % Rotamer: Outliers : 1.47 % Allowed : 14.50 % Favored : 84.03 % 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: -0.56 (0.17), residues: 2583 helix: 2.16 (0.24), residues: 453 sheet: -0.12 (0.19), residues: 702 loop : -1.40 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 594 TYR 0.018 0.001 TYR A 401 PHE 0.015 0.002 PHE H 78 TRP 0.022 0.001 TRP A 345 HIS 0.003 0.001 HIS 6 364 Details of bonding type rmsd covalent geometry : bond 0.00357 (23376) covalent geometry : angle 0.61530 (31764) SS BOND : bond 0.00448 ( 33) SS BOND : angle 0.93849 ( 66) hydrogen bonds : bond 0.03934 ( 780) hydrogen bonds : angle 5.12904 ( 2007) link_ALPHA1-2 : bond 0.00379 ( 6) link_ALPHA1-2 : angle 1.50917 ( 18) link_ALPHA1-3 : bond 0.01146 ( 12) link_ALPHA1-3 : angle 1.78045 ( 36) link_ALPHA1-6 : bond 0.00815 ( 12) link_ALPHA1-6 : angle 1.71479 ( 36) link_BETA1-4 : bond 0.00492 ( 48) link_BETA1-4 : angle 1.30511 ( 144) link_BETA1-6 : bond 0.00563 ( 9) link_BETA1-6 : angle 1.11502 ( 27) link_NAG-ASN : bond 0.00315 ( 75) link_NAG-ASN : angle 2.01345 ( 225) link_TRANS : bond 0.00098 ( 9) link_TRANS : angle 0.39422 ( 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 273 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7919 (tp30) cc_final: 0.7479 (tp30) REVERT: A 203 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: A 290 TRP cc_start: 0.8513 (m100) cc_final: 0.8122 (m100) REVERT: B 609 ASN cc_start: 0.7185 (m-40) cc_final: 0.6945 (m-40) REVERT: B 668 MET cc_start: 0.6185 (tpt) cc_final: 0.5779 (tpp) REVERT: H 32 CYS cc_start: 0.7042 (p) cc_final: 0.6816 (m) REVERT: H 46 GLU cc_start: 0.8006 (tt0) cc_final: 0.7623 (pt0) REVERT: Q 221 ASP cc_start: 0.7460 (t0) cc_final: 0.7000 (t70) REVERT: Q 290 TRP cc_start: 0.8491 (m100) cc_final: 0.8122 (m100) REVERT: R 590 ASN cc_start: 0.4649 (m-40) cc_final: 0.4364 (t0) REVERT: R 668 MET cc_start: 0.5820 (tpt) cc_final: 0.5292 (tpp) REVERT: T 69 THR cc_start: 0.8180 (p) cc_final: 0.7920 (p) REVERT: T 79 GLN cc_start: 0.8105 (mm110) cc_final: 0.7833 (mm110) REVERT: 6 91 TRP cc_start: 0.7166 (t-100) cc_final: 0.6663 (t-100) REVERT: 6 95 GLU cc_start: 0.7949 (tp30) cc_final: 0.7374 (tp30) REVERT: 7 667 ASN cc_start: 0.6901 (m-40) cc_final: 0.6504 (t0) REVERT: 7 668 MET cc_start: 0.6191 (tpt) cc_final: 0.5690 (tpp) REVERT: 8 13 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7502 (mmm160) REVERT: 8 64 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8106 (mmmt) REVERT: 9 79 GLN cc_start: 0.7992 (mm110) cc_final: 0.7760 (mm110) outliers start: 34 outliers final: 31 residues processed: 265 average time/residue: 0.1523 time to fit residues: 65.0950 Evaluate side-chains 261 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 203 GLU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 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 R residue 595 VAL Chi-restraints excluded: chain R residue 630 LEU Chi-restraints excluded: chain S residue 48 ILE 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 262 SER Chi-restraints excluded: chain 6 residue 345 TRP Chi-restraints excluded: chain 6 residue 393 THR Chi-restraints excluded: chain 7 residue 595 VAL Chi-restraints excluded: chain 7 residue 620 CYS 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 141 optimal weight: 1.9990 chunk 220 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 171 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 578 GLN R 592 GLN ** R 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN S 105 GLN 7 592 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.166236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127956 restraints weight = 32186.878| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.90 r_work: 0.3318 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5002 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= 0.166 Angle : 0.661 9.040 32343 Z= 0.324 Chirality : 0.044 0.287 3993 Planarity : 0.004 0.058 3801 Dihedral : 7.462 59.566 6108 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.31 % Favored : 93.19 % Rotamer: Outliers : 1.60 % Allowed : 14.50 % Favored : 83.90 % 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: -0.62 (0.17), residues: 2583 helix: 2.18 (0.24), residues: 453 sheet: -0.15 (0.19), residues: 702 loop : -1.46 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 594 TYR 0.020 0.001 TYR A 401 PHE 0.015 0.002 PHE S 78 TRP 0.024 0.001 TRP Q 345 HIS 0.003 0.001 HIS Q 364 Details of bonding type rmsd covalent geometry : bond 0.00396 (23376) covalent geometry : angle 0.62798 (31764) SS BOND : bond 0.00523 ( 33) SS BOND : angle 1.02994 ( 66) hydrogen bonds : bond 0.03969 ( 780) hydrogen bonds : angle 5.20064 ( 2007) link_ALPHA1-2 : bond 0.00354 ( 6) link_ALPHA1-2 : angle 1.53582 ( 18) link_ALPHA1-3 : bond 0.01126 ( 12) link_ALPHA1-3 : angle 1.75578 ( 36) link_ALPHA1-6 : bond 0.00715 ( 12) link_ALPHA1-6 : angle 1.65215 ( 36) link_BETA1-4 : bond 0.00495 ( 48) link_BETA1-4 : angle 1.34302 ( 144) link_BETA1-6 : bond 0.00520 ( 9) link_BETA1-6 : angle 1.14460 ( 27) link_NAG-ASN : bond 0.00316 ( 75) link_NAG-ASN : angle 2.08864 ( 225) link_TRANS : bond 0.00111 ( 9) link_TRANS : angle 0.42626 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4827.09 seconds wall clock time: 83 minutes 57.73 seconds (5037.73 seconds total)