Starting phenix.real_space_refine on Fri Jun 20 00:47:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4g_25676/06_2025/7t4g_25676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4g_25676/06_2025/7t4g_25676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4g_25676/06_2025/7t4g_25676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4g_25676/06_2025/7t4g_25676.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4g_25676/06_2025/7t4g_25676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4g_25676/06_2025/7t4g_25676.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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 14367 2.51 5 N 3696 2.21 5 O 4835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23045 Number of models: 1 Model: "" Number of chains: 57 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} 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: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "D" 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: "G" 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} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" 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: "E" 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: "F" 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: "J" 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} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" 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: "Q" 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: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" 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: "b" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "f" 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: "g" 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: "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: 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: "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: "m" 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "p" 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: "q" 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: "r" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "w" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" 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: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 13.82, per 1000 atoms: 0.60 Number of scatterers: 23045 At special positions: 0 Unit cell: (156.4, 155.25, 124.2, 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 4835 8.00 N 3696 7.00 C 14367 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=2.06 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 459 " distance=2.04 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 C 101 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 211 " distance=2.02 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 168 " distance=2.02 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 263 " distance=2.05 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 255 " distance=2.08 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 344 " distance=2.02 Simple disulfide: pdb=" SG CYS C 395 " - pdb=" SG CYS C 459 " distance=2.04 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS G 100C" - pdb=" SG CYS G 100K" distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 220 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 211 " distance=1.79 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 168 " distance=2.02 Simple disulfide: pdb=" SG CYS E 194 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 233 " - pdb=" SG CYS E 263 " distance=2.04 Simple disulfide: pdb=" SG CYS E 243 " - pdb=" SG CYS E 255 " distance=2.05 Simple disulfide: pdb=" SG CYS E 311 " - pdb=" SG CYS E 344 " distance=2.07 Simple disulfide: pdb=" SG CYS E 395 " - pdb=" SG CYS E 459 " distance=2.06 Simple disulfide: pdb=" SG CYS E 402 " - pdb=" SG CYS E 432 " distance=2.02 Simple disulfide: pdb=" SG CYS J 100C" - pdb=" SG CYS J 100K" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 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 M 5 " - " MAN M 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN Z 5 " - " MAN Z 6 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN m 5 " - " MAN m 6 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " ALPHA1-3 " BMA M 3 " - " MAN M 8 " " MAN M 4 " - " MAN M 5 " " BMA R 3 " - " MAN R 4 " " BMA Z 3 " - " MAN Z 8 " " MAN Z 4 " - " MAN Z 5 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " BMA m 3 " - " MAN m 8 " " MAN m 4 " - " MAN m 5 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " MAN M 4 " - " MAN M 7 " " BMA R 3 " - " MAN R 7 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 7 " " BMA e 3 " - " MAN e 7 " " BMA f 3 " - " MAN f 5 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 7 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " 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 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " BETA1-6 " NAG O 1 " - " FUC O 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG Q 1 " - " FUC Q 3 " " NAG V 1 " - " FUC V 3 " " NAG b 1 " - " FUC b 3 " " NAG c 1 " - " FUC c 3 " " NAG d 1 " - " FUC d 3 " " NAG i 1 " - " FUC i 3 " " NAG o 1 " - " FUC o 3 " " NAG p 1 " - " FUC p 3 " " NAG q 1 " - " FUC q 3 " " NAG v 1 " - " FUC v 3 " NAG-ASN " 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 B 701 " - " ASN B 627 " " NAG B 702 " - " ASN B 636 " " NAG B 703 " - " ASN B 652 " " NAG C 601 " - " ASN C 70 " " NAG C 602 " - " ASN C 79 " " NAG C 603 " - " ASN C 171 " " NAG C 604 " - " ASN C 184 " " NAG C 605 " - " ASN C 198 " " NAG C 606 " - " ASN C 202 " " NAG C 607 " - " ASN C 244 " " NAG C 608 " - " ASN C 306 " " NAG C 609 " - " ASN C 476 " " NAG D 701 " - " ASN D 627 " " NAG D 702 " - " ASN D 636 " " NAG D 703 " - " ASN D 652 " " NAG E 601 " - " ASN E 70 " " NAG E 602 " - " ASN E 79 " " NAG E 603 " - " ASN E 171 " " NAG E 604 " - " ASN E 184 " " NAG E 605 " - " ASN E 198 " " NAG E 606 " - " ASN E 202 " " NAG E 607 " - " ASN E 244 " " NAG E 608 " - " ASN E 306 " " NAG E 609 " - " ASN E 476 " " NAG F 701 " - " ASN F 627 " " NAG F 702 " - " ASN F 636 " " NAG F 703 " - " ASN F 652 " " NAG M 1 " - " ASN A 37 " " NAG N 1 " - " ASN A 114 " " NAG O 1 " - " ASN A 146 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 212 " " NAG R 1 " - " ASN A 278 " " NAG S 1 " - " ASN A 284 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 316 " " NAG V 1 " - " ASN A 371 " " NAG W 1 " - " ASN A 377 " " NAG X 1 " - " ASN A 460 " " NAG Y 1 " - " ASN A 479 " " NAG Z 1 " - " ASN C 37 " " NAG a 1 " - " ASN C 114 " " NAG b 1 " - " ASN C 146 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 212 " " NAG e 1 " - " ASN C 278 " " NAG f 1 " - " ASN C 284 " " NAG g 1 " - " ASN C 295 " " NAG h 1 " - " ASN C 316 " " NAG i 1 " - " ASN C 371 " " NAG j 1 " - " ASN C 377 " " NAG k 1 " - " ASN C 460 " " NAG l 1 " - " ASN C 479 " " NAG m 1 " - " ASN E 37 " " NAG n 1 " - " ASN E 114 " " NAG o 1 " - " ASN E 146 " " NAG p 1 " - " ASN E 156 " " NAG q 1 " - " ASN E 212 " " NAG r 1 " - " ASN E 278 " " NAG s 1 " - " ASN E 284 " " NAG t 1 " - " ASN E 295 " " NAG u 1 " - " ASN E 316 " " NAG v 1 " - " ASN E 371 " " NAG w 1 " - " ASN E 377 " " NAG x 1 " - " ASN E 460 " " NAG y 1 " - " ASN E 479 " Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 2.5 seconds 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 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: 64 helices and 45 sheets defined 23.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 80 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: 3.772A pdb=" N ILE A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.564A pdb=" N PHE A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'B' and resid 535 through 540 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 584 through 611 removed outlier: 3.705A pdb=" N THR B 588 " --> pdb=" O THR B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 646 through 674 removed outlier: 3.748A pdb=" N ASN B 652 " --> pdb=" O PHE B 648 " (cutoff:3.500A) removed outlier: 4.012A 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 'L' and resid 79 through 83 removed outlier: 4.165A pdb=" N GLY L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 349 through 363 Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.599A pdb=" N ILE C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 404 through 412 Processing helix chain 'C' and resid 485 through 488 Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 553 through 573 Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 585 through 612 Processing helix chain 'D' and resid 638 through 644 Processing helix chain 'D' and resid 646 through 674 removed outlier: 3.975A pdb=" N GLU D 651 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN D 652 " --> pdb=" O PHE D 648 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA D 655 " --> pdb=" O GLU D 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'E' and resid 51 through 57 Processing helix chain 'E' and resid 80 through 99 removed outlier: 3.663A pdb=" N ILE E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 349 through 363 Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.599A pdb=" N ILE E 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.599A pdb=" N PHE E 390 " --> pdb=" O PRO E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 485 through 488 Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'F' and resid 535 through 541 removed outlier: 4.305A pdb=" N THR F 540 " --> pdb=" O PHE F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 573 Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 584 through 612 Processing helix chain 'F' and resid 638 through 644 Processing helix chain 'F' and resid 646 through 674 removed outlier: 3.942A pdb=" N GLU F 651 " --> pdb=" O ASP F 647 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN F 652 " --> pdb=" O PHE F 648 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA F 655 " --> pdb=" O GLU F 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.209A pdb=" N VAL A 258 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.668A pdb=" N CYS A 44 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.934A pdb=" N PHE A 75 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 188 Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA7, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.740A pdb=" N GLN A 217 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 277 removed outlier: 7.322A pdb=" N THR A 379 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 288 through 290 removed outlier: 5.770A pdb=" N GLY A 455 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 315 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 399 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 323 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.032A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.441A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.682A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.848A pdb=" N GLY L 13 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AB8, first strand: chain 'C' and resid 35 through 37 removed outlier: 4.099A pdb=" N VAL C 258 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 59 Processing sheet with id=AC1, first strand: chain 'C' and resid 73 through 76 removed outlier: 4.910A pdb=" N PHE C 75 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 180 through 188 Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AC4, first strand: chain 'C' and resid 217 through 218 removed outlier: 6.629A pdb=" N GLN C 217 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 275 through 277 removed outlier: 7.283A pdb=" N THR C 379 " --> pdb=" O MET C 482 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.043A pdb=" N GLY C 455 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY C 315 " --> pdb=" O GLY C 455 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C 399 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 320 through 323 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.024A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 96 through 97 Processing sheet with id=AD2, first strand: chain 'I' and resid 4 through 7 removed outlier: 5.440A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLN I 27 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER I 67 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N ILE I 29 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N SER I 65 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 13 removed outlier: 4.025A pdb=" N GLY I 13 " --> pdb=" O ASP I 104 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 29 through 30 Processing sheet with id=AD5, first strand: chain 'E' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL E 258 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.855A pdb=" N CYS E 44 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 73 through 76 removed outlier: 4.907A pdb=" N PHE E 75 " --> pdb=" O PRO E 253 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 180 through 188 Processing sheet with id=AD9, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AE1, first strand: chain 'E' and resid 217 through 218 removed outlier: 6.644A pdb=" N GLN E 217 " --> pdb=" O TYR E 449 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 275 through 277 removed outlier: 7.387A pdb=" N THR E 379 " --> pdb=" O MET E 482 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 288 through 290 removed outlier: 5.845A pdb=" N GLY E 455 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY E 315 " --> pdb=" O GLY E 455 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 399 " --> pdb=" O ARG E 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 320 through 323 Processing sheet with id=AE5, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 5.992A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 removed outlier: 5.344A pdb=" N THR K 69 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLN K 27 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N SER K 67 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N ILE K 29 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 11.934A pdb=" N SER K 65 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.985A pdb=" N GLY K 13 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2049 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: 8.16 Time building geometry restraints manager: 8.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4718 1.32 - 1.47: 8416 1.47 - 1.61: 10194 1.61 - 1.76: 37 1.76 - 1.90: 169 Bond restraints: 23534 Sorted by residual: bond pdb=" CA VAL F 573 " pdb=" CB VAL F 573 " ideal model delta sigma weight residual 1.537 1.575 -0.038 5.00e-03 4.00e+04 5.83e+01 bond pdb=" CA VAL D 573 " pdb=" CB VAL D 573 " ideal model delta sigma weight residual 1.539 1.573 -0.034 5.40e-03 3.43e+04 4.08e+01 bond pdb=" CB LEU D 674 " pdb=" CG LEU D 674 " ideal model delta sigma weight residual 1.530 1.642 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CB LEU B 674 " pdb=" CG LEU B 674 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" CB LEU F 674 " pdb=" CG LEU F 674 " ideal model delta sigma weight residual 1.530 1.637 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 23529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 26035 2.18 - 4.36: 4863 4.36 - 6.55: 943 6.55 - 8.73: 124 8.73 - 10.91: 30 Bond angle restraints: 31995 Sorted by residual: angle pdb=" N VAL E 32 " pdb=" CA VAL E 32 " pdb=" C VAL E 32 " ideal model delta sigma weight residual 108.63 116.68 -8.05 8.60e-01 1.35e+00 8.75e+01 angle pdb=" C VAL B 573 " pdb=" N PRO B 574 " pdb=" CA PRO B 574 " ideal model delta sigma weight residual 119.56 128.63 -9.07 1.02e+00 9.61e-01 7.91e+01 angle pdb=" C VAL D 573 " pdb=" N PRO D 574 " pdb=" CA PRO D 574 " ideal model delta sigma weight residual 119.82 127.61 -7.79 9.80e-01 1.04e+00 6.32e+01 angle pdb=" C VAL F 573 " pdb=" N PRO F 574 " pdb=" CA PRO F 574 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" N THR B 588 " pdb=" CA THR B 588 " pdb=" C THR B 588 " ideal model delta sigma weight residual 113.41 103.86 9.55 1.22e+00 6.72e-01 6.13e+01 ... (remaining 31990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 15594 21.43 - 42.85: 403 42.85 - 64.28: 94 64.28 - 85.70: 117 85.70 - 107.13: 68 Dihedral angle restraints: 16276 sinusoidal: 8653 harmonic: 7623 Sorted by residual: dihedral pdb=" CB CYS E 243 " pdb=" SG CYS E 243 " pdb=" SG CYS E 255 " pdb=" CB CYS E 255 " ideal model delta sinusoidal sigma weight residual 93.00 -176.51 -90.49 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS C 243 " pdb=" SG CYS C 243 " pdb=" SG CYS C 255 " pdb=" CB CYS C 255 " ideal model delta sinusoidal sigma weight residual -86.00 -176.32 90.32 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 243 " pdb=" SG CYS A 243 " pdb=" SG CYS A 255 " pdb=" CB CYS A 255 " ideal model delta sinusoidal sigma weight residual 93.00 -177.26 -89.74 1 1.00e+01 1.00e-02 9.56e+01 ... (remaining 16273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2544 0.107 - 0.214: 946 0.214 - 0.320: 361 0.320 - 0.427: 139 0.427 - 0.534: 68 Chirality restraints: 4058 Sorted by residual: chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 6.11e+02 chirality pdb=" C1 MAN R 6 " pdb=" O2 MAN R 5 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 2.02 0.38 2.00e-02 2.50e+03 3.52e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.27e+02 ... (remaining 4055 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG t 2 " 0.217 2.00e-02 2.50e+03 1.80e-01 4.07e+02 pdb=" C7 NAG t 2 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG t 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG t 2 " -0.297 2.00e-02 2.50e+03 pdb=" O7 NAG t 2 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.168 2.00e-02 2.50e+03 1.41e-01 2.48e+02 pdb=" C7 NAG R 1 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 371 " -0.137 2.00e-02 2.50e+03 1.36e-01 2.33e+02 pdb=" CG ASN C 371 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 371 " 0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN C 371 " 0.200 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.168 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7757 2.87 - 3.38: 20792 3.38 - 3.89: 39341 3.89 - 4.39: 45462 4.39 - 4.90: 72437 Nonbonded interactions: 185789 Sorted by model distance: nonbonded pdb=" OD1 ASP C 89 " pdb=" NZ LYS D 589 " model vdw 2.363 3.120 nonbonded pdb=" C4 BMA R 3 " pdb=" O6 BMA R 3 " model vdw 2.446 2.776 nonbonded pdb=" N THR C 246 " pdb=" N ASN C 247 " model vdw 2.447 2.560 nonbonded pdb=" N ARG B 582 " pdb=" N LEU B 583 " model vdw 2.451 2.560 nonbonded pdb=" N THR A 246 " pdb=" N ASN A 247 " model vdw 2.452 2.560 ... (remaining 185784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 2 or resid 5 through 8)) selection = (chain 'R' and (resid 1 or resid 4 through 7)) selection = (chain 'Z' and (resid 2 or resid 5 through 8)) selection = (chain 'e' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 2 or resid 5 through 8)) selection = (chain 'r' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'u' selection = chain 'x' } ncs_group { reference = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) selection = (chain 'y' and resid 1 through 2) } ncs_group { reference = chain 'S' selection = chain 's' selection = chain 't' selection = chain 'w' } 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 group one per residue 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 53.420 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 0.252 23742 Z= 1.194 Angle : 1.877 12.694 32586 Z= 1.175 Chirality : 0.149 0.534 4058 Planarity : 0.010 0.180 3813 Dihedral : 14.435 107.127 11269 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 1.35 % Allowed : 2.85 % Favored : 95.80 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2595 helix: -0.06 (0.21), residues: 471 sheet: 0.69 (0.19), residues: 654 loop : -0.45 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.008 TRP F 586 HIS 0.008 0.003 HIS G 100N PHE 0.039 0.007 PHE B 537 TYR 0.055 0.008 TYR H 91 ARG 0.012 0.001 ARG C 231 Details of bonding type rmsd link_NAG-ASN : bond 0.07541 ( 75) link_NAG-ASN : angle 3.14362 ( 225) link_ALPHA1-6 : bond 0.05372 ( 12) link_ALPHA1-6 : angle 3.43268 ( 36) link_BETA1-4 : bond 0.06553 ( 55) link_BETA1-4 : angle 4.23650 ( 165) link_ALPHA1-2 : bond 0.07063 ( 9) link_ALPHA1-2 : angle 4.10294 ( 27) link_ALPHA1-3 : bond 0.07136 ( 12) link_ALPHA1-3 : angle 4.09985 ( 36) hydrogen bonds : bond 0.19221 ( 782) hydrogen bonds : angle 7.27097 ( 2049) link_BETA1-6 : bond 0.05746 ( 12) link_BETA1-6 : angle 3.31251 ( 36) SS BOND : bond 0.06220 ( 33) SS BOND : angle 2.79276 ( 66) covalent geometry : bond 0.02216 (23534) covalent geometry : angle 1.83076 (31995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 581 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8385 (m-10) cc_final: 0.8118 (m-10) REVERT: A 163 GLU cc_start: 0.7552 (tp30) cc_final: 0.7335 (tp30) REVERT: A 391 MET cc_start: 0.8515 (ttp) cc_final: 0.8133 (ttm) REVERT: B 592 GLN cc_start: 0.6083 (tp40) cc_final: 0.5639 (tm-30) REVERT: H 55 ASP cc_start: 0.8567 (m-30) cc_final: 0.8281 (p0) REVERT: H 60 ASN cc_start: 0.8382 (t0) cc_final: 0.8150 (t0) REVERT: H 69 ILE cc_start: 0.8910 (mt) cc_final: 0.8543 (mt) REVERT: L 101 THR cc_start: 0.7782 (p) cc_final: 0.7364 (t) REVERT: C 48 ASN cc_start: 0.8024 (t0) cc_final: 0.7772 (p0) REVERT: C 56 GLN cc_start: 0.7323 (mt0) cc_final: 0.7073 (mp10) REVERT: C 265 ARG cc_start: 0.8806 (ptp90) cc_final: 0.8022 (ptp-170) REVERT: D 559 LEU cc_start: 0.8780 (tp) cc_final: 0.8423 (tt) REVERT: D 589 LYS cc_start: 0.8421 (mtpt) cc_final: 0.7803 (mtmt) REVERT: D 603 LYS cc_start: 0.8929 (tttm) cc_final: 0.8662 (tptt) REVERT: D 631 ILE cc_start: 0.9224 (mm) cc_final: 0.8951 (pt) REVERT: G 55 ASP cc_start: 0.8689 (m-30) cc_final: 0.8469 (m-30) REVERT: G 90 TYR cc_start: 0.7696 (m-80) cc_final: 0.7377 (m-80) REVERT: I 19 VAL cc_start: 0.6728 (t) cc_final: 0.6517 (p) REVERT: I 74 THR cc_start: 0.7341 (m) cc_final: 0.6703 (p) REVERT: I 79 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6979 (tm-30) REVERT: I 87 TYR cc_start: 0.8943 (m-80) cc_final: 0.8581 (m-80) REVERT: E 290 TRP cc_start: 0.8699 (m100) cc_final: 0.8431 (m100) REVERT: E 391 MET cc_start: 0.8824 (ttp) cc_final: 0.8584 (ttt) REVERT: F 557 ARG cc_start: 0.7724 (ptt180) cc_final: 0.7370 (ptt90) REVERT: F 588 THR cc_start: 0.7428 (m) cc_final: 0.7155 (p) REVERT: F 633 LYS cc_start: 0.7977 (mttp) cc_final: 0.7771 (mmtt) REVERT: F 668 MET cc_start: 0.8797 (mmm) cc_final: 0.8543 (mmp) REVERT: J 54 ASN cc_start: 0.8052 (t0) cc_final: 0.7800 (p0) REVERT: J 100 TYR cc_start: 0.8719 (m-80) cc_final: 0.8469 (m-80) REVERT: K 4 LEU cc_start: 0.8586 (tp) cc_final: 0.8368 (tp) REVERT: K 19 VAL cc_start: 0.8291 (t) cc_final: 0.7992 (t) REVERT: K 24 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7541 (mtt-85) outliers start: 6 outliers final: 2 residues processed: 585 average time/residue: 0.4155 time to fit residues: 363.0829 Evaluate side-chains 291 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain E residue 476 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 291 HIS A 336 ASN A 394 ASN B 635 ASN B 661 GLN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN H 76 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 89 GLN C 210 HIS C 270 GLN C 291 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 76 ASN G 77 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 HIS ** F 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.109091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085677 restraints weight = 51508.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085840 restraints weight = 40373.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086861 restraints weight = 43196.288| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 23742 Z= 0.231 Angle : 0.908 14.016 32586 Z= 0.446 Chirality : 0.051 0.529 4058 Planarity : 0.005 0.083 3813 Dihedral : 11.993 88.181 6368 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.12 % Favored : 95.41 % Rotamer: Outliers : 2.29 % Allowed : 8.79 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2595 helix: 1.16 (0.24), residues: 453 sheet: 0.43 (0.20), residues: 639 loop : -0.80 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 121 HIS 0.008 0.002 HIS A 291 PHE 0.023 0.002 PHE B 537 TYR 0.026 0.002 TYR L 91 ARG 0.010 0.001 ARG E 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 75) link_NAG-ASN : angle 3.27861 ( 225) link_ALPHA1-6 : bond 0.00422 ( 12) link_ALPHA1-6 : angle 1.50665 ( 36) link_BETA1-4 : bond 0.00560 ( 55) link_BETA1-4 : angle 2.52854 ( 165) link_ALPHA1-2 : bond 0.00437 ( 9) link_ALPHA1-2 : angle 2.28740 ( 27) link_ALPHA1-3 : bond 0.00927 ( 12) link_ALPHA1-3 : angle 2.33464 ( 36) hydrogen bonds : bond 0.06777 ( 782) hydrogen bonds : angle 6.00887 ( 2049) link_BETA1-6 : bond 0.00636 ( 12) link_BETA1-6 : angle 1.27158 ( 36) SS BOND : bond 0.00449 ( 33) SS BOND : angle 1.14445 ( 66) covalent geometry : bond 0.00524 (23534) covalent geometry : angle 0.84512 (31995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 318 time to evaluate : 4.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7432 (t0) cc_final: 0.6871 (m-40) REVERT: A 391 MET cc_start: 0.8103 (ttp) cc_final: 0.7796 (ttt) REVERT: A 483 SER cc_start: 0.9148 (t) cc_final: 0.8927 (t) REVERT: B 591 LEU cc_start: 0.5636 (tp) cc_final: 0.5405 (tt) REVERT: L 36 TYR cc_start: 0.8558 (m-80) cc_final: 0.8287 (m-80) REVERT: L 47 LEU cc_start: 0.8807 (mt) cc_final: 0.8430 (mt) REVERT: L 48 ILE cc_start: 0.8624 (mm) cc_final: 0.8414 (mt) REVERT: C 232 TYR cc_start: 0.8098 (m-80) cc_final: 0.7813 (m-80) REVERT: D 631 ILE cc_start: 0.8958 (mm) cc_final: 0.8702 (pt) REVERT: G 100 ASN cc_start: 0.8497 (m-40) cc_final: 0.8234 (m110) REVERT: E 290 TRP cc_start: 0.8463 (m100) cc_final: 0.8245 (m100) REVERT: E 391 MET cc_start: 0.8333 (ttp) cc_final: 0.8077 (ttt) REVERT: F 668 MET cc_start: 0.8666 (mmm) cc_final: 0.8433 (mmt) REVERT: J 75 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8307 (tptp) REVERT: K 24 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7183 (mtm-85) outliers start: 53 outliers final: 26 residues processed: 358 average time/residue: 0.4455 time to fit residues: 249.6604 Evaluate side-chains 271 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 1 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 566 GLN B 635 ASN C 48 ASN C 394 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN E 336 ASN E 394 ASN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084167 restraints weight = 51457.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084389 restraints weight = 41106.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085263 restraints weight = 40777.030| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23742 Z= 0.192 Angle : 0.785 11.304 32586 Z= 0.384 Chirality : 0.048 0.463 4058 Planarity : 0.004 0.043 3813 Dihedral : 10.046 79.394 6368 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.55 % Favored : 94.99 % Rotamer: Outliers : 2.42 % Allowed : 9.22 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2595 helix: 0.90 (0.23), residues: 481 sheet: 0.25 (0.18), residues: 750 loop : -1.22 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 91 HIS 0.004 0.001 HIS E 364 PHE 0.017 0.002 PHE B 537 TYR 0.029 0.002 TYR K 91 ARG 0.013 0.001 ARG A 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 75) link_NAG-ASN : angle 2.73503 ( 225) link_ALPHA1-6 : bond 0.00708 ( 12) link_ALPHA1-6 : angle 1.78784 ( 36) link_BETA1-4 : bond 0.00575 ( 55) link_BETA1-4 : angle 1.95277 ( 165) link_ALPHA1-2 : bond 0.00516 ( 9) link_ALPHA1-2 : angle 1.77125 ( 27) link_ALPHA1-3 : bond 0.01050 ( 12) link_ALPHA1-3 : angle 2.02967 ( 36) hydrogen bonds : bond 0.05497 ( 782) hydrogen bonds : angle 5.57206 ( 2049) link_BETA1-6 : bond 0.00651 ( 12) link_BETA1-6 : angle 1.30863 ( 36) SS BOND : bond 0.00402 ( 33) SS BOND : angle 0.95005 ( 66) covalent geometry : bond 0.00427 (23534) covalent geometry : angle 0.73488 (31995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 2.557 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 48 ASN cc_start: 0.7360 (t0) cc_final: 0.6900 (m-40) REVERT: A 391 MET cc_start: 0.8217 (ttp) cc_final: 0.7901 (ttt) REVERT: A 483 SER cc_start: 0.9075 (t) cc_final: 0.8871 (t) REVERT: B 545 MET cc_start: 0.8437 (mmm) cc_final: 0.7681 (tpp) REVERT: B 668 MET cc_start: 0.8084 (mmm) cc_final: 0.7841 (tpt) REVERT: H 43 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8363 (mmtm) REVERT: L 36 TYR cc_start: 0.8586 (m-80) cc_final: 0.8377 (m-80) REVERT: L 78 LEU cc_start: 0.9147 (tp) cc_final: 0.8892 (tt) REVERT: L 91 TYR cc_start: 0.8287 (p90) cc_final: 0.8034 (p90) REVERT: D 556 SER cc_start: 0.8788 (m) cc_final: 0.8085 (t) REVERT: D 559 LEU cc_start: 0.8716 (tp) cc_final: 0.8365 (tt) REVERT: D 603 LYS cc_start: 0.8618 (tptp) cc_final: 0.8390 (tppt) REVERT: D 631 ILE cc_start: 0.8853 (mm) cc_final: 0.8643 (pt) REVERT: G 100 ASN cc_start: 0.8635 (m-40) cc_final: 0.8361 (m-40) REVERT: I 55 GLN cc_start: 0.7976 (tp40) cc_final: 0.7715 (tp-100) REVERT: I 79 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7654 (tm-30) REVERT: I 82 ASP cc_start: 0.7250 (m-30) cc_final: 0.6987 (m-30) REVERT: E 290 TRP cc_start: 0.8481 (m100) cc_final: 0.8256 (m100) REVERT: E 391 MET cc_start: 0.8378 (ttp) cc_final: 0.8096 (ttt) REVERT: F 668 MET cc_start: 0.8599 (mmm) cc_final: 0.8287 (mmt) REVERT: J 75 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8268 (tptp) REVERT: J 91 TYR cc_start: 0.7657 (m-80) cc_final: 0.7444 (m-10) REVERT: J 100 TYR cc_start: 0.8456 (m-80) cc_final: 0.8213 (m-80) REVERT: K 24 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.7125 (mtm-85) outliers start: 56 outliers final: 40 residues processed: 318 average time/residue: 0.3665 time to fit residues: 182.0597 Evaluate side-chains 287 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 153 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 270 GLN C 394 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.107393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084023 restraints weight = 51712.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084236 restraints weight = 40797.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.084968 restraints weight = 41426.955| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23742 Z= 0.161 Angle : 0.720 10.330 32586 Z= 0.349 Chirality : 0.046 0.421 4058 Planarity : 0.004 0.044 3813 Dihedral : 8.742 73.074 6366 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.97 % Favored : 94.57 % Rotamer: Outliers : 2.51 % Allowed : 10.13 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2595 helix: 1.13 (0.24), residues: 475 sheet: 0.20 (0.18), residues: 744 loop : -1.25 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 345 HIS 0.004 0.001 HIS E 364 PHE 0.019 0.002 PHE E 346 TYR 0.031 0.002 TYR I 91 ARG 0.006 0.001 ARG F 594 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 75) link_NAG-ASN : angle 2.45239 ( 225) link_ALPHA1-6 : bond 0.00823 ( 12) link_ALPHA1-6 : angle 1.97637 ( 36) link_BETA1-4 : bond 0.00508 ( 55) link_BETA1-4 : angle 1.73179 ( 165) link_ALPHA1-2 : bond 0.00399 ( 9) link_ALPHA1-2 : angle 1.68096 ( 27) link_ALPHA1-3 : bond 0.00891 ( 12) link_ALPHA1-3 : angle 2.04175 ( 36) hydrogen bonds : bond 0.04899 ( 782) hydrogen bonds : angle 5.32906 ( 2049) link_BETA1-6 : bond 0.00619 ( 12) link_BETA1-6 : angle 1.26251 ( 36) SS BOND : bond 0.00344 ( 33) SS BOND : angle 0.79308 ( 66) covalent geometry : bond 0.00359 (23534) covalent geometry : angle 0.67521 (31995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 2.410 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 48 ASN cc_start: 0.7391 (t0) cc_final: 0.6979 (m-40) REVERT: A 391 MET cc_start: 0.8279 (ttp) cc_final: 0.7994 (ttt) REVERT: L 91 TYR cc_start: 0.8347 (p90) cc_final: 0.7622 (p90) REVERT: D 556 SER cc_start: 0.8823 (m) cc_final: 0.8154 (t) REVERT: D 629 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7337 (t) REVERT: G 100 ASN cc_start: 0.8523 (m-40) cc_final: 0.8279 (m-40) REVERT: I 58 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8150 (p) REVERT: I 79 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7522 (tm-30) REVERT: E 144 MET cc_start: 0.8137 (mpp) cc_final: 0.7854 (mmt) REVERT: E 172 MET cc_start: 0.7762 (tpt) cc_final: 0.7532 (tpt) REVERT: E 391 MET cc_start: 0.8349 (ttp) cc_final: 0.8082 (ttt) REVERT: F 668 MET cc_start: 0.8564 (mmm) cc_final: 0.8196 (mmt) REVERT: J 75 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8268 (tptp) REVERT: J 91 TYR cc_start: 0.7650 (m-80) cc_final: 0.7340 (m-10) REVERT: J 94 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7673 (ttm-80) REVERT: K 24 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.7233 (mtt180) outliers start: 58 outliers final: 40 residues processed: 314 average time/residue: 0.3673 time to fit residues: 180.3380 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 : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.105811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082072 restraints weight = 52123.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.082201 restraints weight = 42314.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083084 restraints weight = 43181.193| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23742 Z= 0.185 Angle : 0.720 9.940 32586 Z= 0.349 Chirality : 0.046 0.413 4058 Planarity : 0.004 0.054 3813 Dihedral : 8.245 69.672 6366 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.16 % Favored : 94.41 % Rotamer: Outliers : 2.55 % Allowed : 11.30 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2595 helix: 1.23 (0.24), residues: 469 sheet: 0.13 (0.19), residues: 729 loop : -1.32 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 52 HIS 0.004 0.001 HIS E 364 PHE 0.020 0.002 PHE E 346 TYR 0.029 0.002 TYR K 91 ARG 0.004 0.000 ARG F 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 75) link_NAG-ASN : angle 2.35170 ( 225) link_ALPHA1-6 : bond 0.00840 ( 12) link_ALPHA1-6 : angle 2.06104 ( 36) link_BETA1-4 : bond 0.00468 ( 55) link_BETA1-4 : angle 1.62421 ( 165) link_ALPHA1-2 : bond 0.00411 ( 9) link_ALPHA1-2 : angle 1.64403 ( 27) link_ALPHA1-3 : bond 0.00843 ( 12) link_ALPHA1-3 : angle 2.07617 ( 36) hydrogen bonds : bond 0.04812 ( 782) hydrogen bonds : angle 5.26089 ( 2049) link_BETA1-6 : bond 0.00563 ( 12) link_BETA1-6 : angle 1.29804 ( 36) SS BOND : bond 0.00407 ( 33) SS BOND : angle 0.86313 ( 66) covalent geometry : bond 0.00425 (23534) covalent geometry : angle 0.67850 (31995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 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: 59 poor density : 255 time to evaluate : 2.534 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 48 ASN cc_start: 0.7450 (t0) cc_final: 0.7051 (m-40) REVERT: A 391 MET cc_start: 0.8168 (ttp) cc_final: 0.7858 (ttt) REVERT: B 545 MET cc_start: 0.8456 (mmm) cc_final: 0.7804 (tpp) REVERT: L 18 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: L 91 TYR cc_start: 0.8525 (p90) cc_final: 0.7850 (p90) REVERT: C 309 MET cc_start: 0.8871 (ttp) cc_final: 0.8388 (ttp) REVERT: D 556 SER cc_start: 0.8894 (m) cc_final: 0.8196 (t) REVERT: D 629 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7340 (t) REVERT: G 100 ASN cc_start: 0.8542 (m-40) cc_final: 0.8301 (m-40) REVERT: I 55 GLN cc_start: 0.7803 (tp40) cc_final: 0.7473 (tp-100) REVERT: I 79 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7549 (tm-30) REVERT: I 87 TYR cc_start: 0.8443 (m-80) cc_final: 0.8201 (m-10) REVERT: E 144 MET cc_start: 0.8199 (mpp) cc_final: 0.7950 (mpp) REVERT: E 391 MET cc_start: 0.8426 (ttp) cc_final: 0.8128 (ttt) REVERT: F 557 ARG cc_start: 0.7656 (ptt90) cc_final: 0.6701 (ptp90) REVERT: F 668 MET cc_start: 0.8504 (mmm) cc_final: 0.8162 (mmp) REVERT: J 75 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8202 (tptp) REVERT: J 91 TYR cc_start: 0.7497 (m-80) cc_final: 0.7249 (m-10) outliers start: 59 outliers final: 45 residues processed: 293 average time/residue: 0.3943 time to fit residues: 184.8533 Evaluate side-chains 273 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 24 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100NHIS K 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082706 restraints weight = 51732.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082979 restraints weight = 42177.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083505 restraints weight = 43560.100| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23742 Z= 0.168 Angle : 0.719 17.716 32586 Z= 0.344 Chirality : 0.047 0.669 4058 Planarity : 0.004 0.043 3813 Dihedral : 7.983 66.581 6366 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.32 % Favored : 94.26 % Rotamer: Outliers : 2.55 % Allowed : 11.99 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2595 helix: 1.30 (0.24), residues: 468 sheet: 0.08 (0.19), residues: 732 loop : -1.40 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 52 HIS 0.004 0.001 HIS E 364 PHE 0.024 0.002 PHE E 346 TYR 0.032 0.002 TYR I 91 ARG 0.003 0.000 ARG F 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 75) link_NAG-ASN : angle 2.77300 ( 225) link_ALPHA1-6 : bond 0.00859 ( 12) link_ALPHA1-6 : angle 2.06127 ( 36) link_BETA1-4 : bond 0.00472 ( 55) link_BETA1-4 : angle 1.53206 ( 165) link_ALPHA1-2 : bond 0.00411 ( 9) link_ALPHA1-2 : angle 1.61669 ( 27) link_ALPHA1-3 : bond 0.00886 ( 12) link_ALPHA1-3 : angle 2.03654 ( 36) hydrogen bonds : bond 0.04613 ( 782) hydrogen bonds : angle 5.21958 ( 2049) link_BETA1-6 : bond 0.00576 ( 12) link_BETA1-6 : angle 1.27657 ( 36) SS BOND : bond 0.00366 ( 33) SS BOND : angle 0.82257 ( 66) covalent geometry : bond 0.00381 (23534) covalent geometry : angle 0.66785 (31995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7392 (t0) cc_final: 0.7015 (m-40) REVERT: A 391 MET cc_start: 0.8149 (ttp) cc_final: 0.7799 (ttt) REVERT: B 545 MET cc_start: 0.8568 (mmm) cc_final: 0.7900 (tpp) REVERT: L 18 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: L 91 TYR cc_start: 0.8535 (p90) cc_final: 0.7847 (p90) REVERT: D 571 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7356 (tt) REVERT: D 629 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7200 (t) REVERT: G 100 ASN cc_start: 0.8540 (m-40) cc_final: 0.8307 (m-40) REVERT: I 79 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7601 (tm-30) REVERT: I 87 TYR cc_start: 0.8445 (m-80) cc_final: 0.8206 (m-10) REVERT: E 391 MET cc_start: 0.8439 (ttp) cc_final: 0.8157 (ttt) REVERT: E 483 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8794 (t) REVERT: F 557 ARG cc_start: 0.7682 (ptt90) cc_final: 0.6733 (ptp90) REVERT: F 633 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7818 (mmtp) REVERT: F 668 MET cc_start: 0.8494 (mmm) cc_final: 0.8148 (mmp) REVERT: J 75 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8239 (tptp) REVERT: J 91 TYR cc_start: 0.7548 (m-80) cc_final: 0.7241 (m-10) outliers start: 59 outliers final: 42 residues processed: 289 average time/residue: 0.3371 time to fit residues: 154.9272 Evaluate side-chains 278 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 13 optimal weight: 3.9990 chunk 254 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 239 optimal weight: 0.0980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN C 394 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.105236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081036 restraints weight = 51977.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081677 restraints weight = 41463.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082297 restraints weight = 41066.143| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23742 Z= 0.196 Angle : 0.734 17.439 32586 Z= 0.352 Chirality : 0.046 0.405 4058 Planarity : 0.004 0.042 3813 Dihedral : 7.831 64.872 6366 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.82 % Favored : 93.76 % Rotamer: Outliers : 2.47 % Allowed : 12.25 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2595 helix: 1.24 (0.24), residues: 468 sheet: 0.10 (0.19), residues: 699 loop : -1.54 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 52 HIS 0.005 0.001 HIS E 364 PHE 0.023 0.002 PHE E 43 TYR 0.036 0.002 TYR I 91 ARG 0.005 0.000 ARG F 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 75) link_NAG-ASN : angle 2.73861 ( 225) link_ALPHA1-6 : bond 0.00825 ( 12) link_ALPHA1-6 : angle 2.08837 ( 36) link_BETA1-4 : bond 0.00451 ( 55) link_BETA1-4 : angle 1.51171 ( 165) link_ALPHA1-2 : bond 0.00402 ( 9) link_ALPHA1-2 : angle 1.63249 ( 27) link_ALPHA1-3 : bond 0.00838 ( 12) link_ALPHA1-3 : angle 2.08984 ( 36) hydrogen bonds : bond 0.04631 ( 782) hydrogen bonds : angle 5.18721 ( 2049) link_BETA1-6 : bond 0.00526 ( 12) link_BETA1-6 : angle 1.28808 ( 36) SS BOND : bond 0.00442 ( 33) SS BOND : angle 0.86949 ( 66) covalent geometry : bond 0.00450 (23534) covalent geometry : angle 0.68473 (31995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7493 (t0) cc_final: 0.7101 (m-40) REVERT: A 391 MET cc_start: 0.8417 (ttp) cc_final: 0.8138 (ttt) REVERT: B 545 MET cc_start: 0.8661 (mmm) cc_final: 0.8096 (tpp) REVERT: L 91 TYR cc_start: 0.8615 (p90) cc_final: 0.7969 (p90) REVERT: C 404 MET cc_start: 0.7564 (mmm) cc_final: 0.6752 (mmm) REVERT: C 497 TYR cc_start: 0.9138 (m-80) cc_final: 0.8335 (m-10) REVERT: D 571 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7305 (tt) REVERT: D 629 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7431 (t) REVERT: I 55 GLN cc_start: 0.8001 (tp40) cc_final: 0.7769 (tp-100) REVERT: I 79 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7528 (tm-30) REVERT: I 87 TYR cc_start: 0.8541 (m-80) cc_final: 0.8208 (m-10) REVERT: E 203 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7513 (mm-30) REVERT: E 391 MET cc_start: 0.8481 (ttp) cc_final: 0.8196 (ttt) REVERT: E 483 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8884 (t) REVERT: F 557 ARG cc_start: 0.7644 (ptt90) cc_final: 0.6661 (ptp90) REVERT: F 633 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7876 (mmtp) REVERT: F 668 MET cc_start: 0.8454 (mmm) cc_final: 0.8066 (mmp) REVERT: J 75 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8291 (tptp) outliers start: 57 outliers final: 46 residues processed: 273 average time/residue: 0.3337 time to fit residues: 143.5750 Evaluate side-chains 270 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 17 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 433 HIS ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081335 restraints weight = 51997.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082170 restraints weight = 41855.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.082945 restraints weight = 37127.382| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23742 Z= 0.172 Angle : 0.713 14.518 32586 Z= 0.342 Chirality : 0.046 0.401 4058 Planarity : 0.004 0.066 3813 Dihedral : 7.518 59.885 6366 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.63 % Favored : 93.95 % Rotamer: Outliers : 2.29 % Allowed : 12.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2595 helix: 1.21 (0.24), residues: 474 sheet: -0.05 (0.19), residues: 702 loop : -1.65 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 52 HIS 0.004 0.001 HIS E 364 PHE 0.015 0.002 PHE A 230 TYR 0.033 0.002 TYR I 91 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 75) link_NAG-ASN : angle 2.46827 ( 225) link_ALPHA1-6 : bond 0.00822 ( 12) link_ALPHA1-6 : angle 1.91833 ( 36) link_BETA1-4 : bond 0.00460 ( 55) link_BETA1-4 : angle 1.45005 ( 165) link_ALPHA1-2 : bond 0.00398 ( 9) link_ALPHA1-2 : angle 1.60408 ( 27) link_ALPHA1-3 : bond 0.00902 ( 12) link_ALPHA1-3 : angle 2.00024 ( 36) hydrogen bonds : bond 0.04478 ( 782) hydrogen bonds : angle 5.14600 ( 2049) link_BETA1-6 : bond 0.00536 ( 12) link_BETA1-6 : angle 1.28617 ( 36) SS BOND : bond 0.00385 ( 33) SS BOND : angle 0.79259 ( 66) covalent geometry : bond 0.00394 (23534) covalent geometry : angle 0.67118 (31995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7516 (t0) cc_final: 0.7184 (m-40) REVERT: A 391 MET cc_start: 0.8152 (ttp) cc_final: 0.7766 (ttt) REVERT: B 545 MET cc_start: 0.8654 (mmm) cc_final: 0.8057 (tpp) REVERT: H 27 ASP cc_start: 0.7458 (t0) cc_final: 0.7233 (t0) REVERT: H 67 ILE cc_start: 0.8956 (tt) cc_final: 0.8727 (tp) REVERT: L 91 TYR cc_start: 0.8522 (p90) cc_final: 0.7980 (p90) REVERT: C 404 MET cc_start: 0.7272 (mmm) cc_final: 0.6764 (mmm) REVERT: D 571 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7432 (tt) REVERT: D 629 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7291 (t) REVERT: I 79 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7428 (tm-30) REVERT: I 87 TYR cc_start: 0.8438 (m-80) cc_final: 0.8139 (m-10) REVERT: E 391 MET cc_start: 0.8439 (ttp) cc_final: 0.8101 (ttt) REVERT: E 483 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8829 (t) REVERT: F 668 MET cc_start: 0.8470 (mmm) cc_final: 0.8020 (mmp) outliers start: 53 outliers final: 42 residues processed: 279 average time/residue: 0.3367 time to fit residues: 149.2103 Evaluate side-chains 265 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 186 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079475 restraints weight = 52263.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080439 restraints weight = 41637.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081093 restraints weight = 43720.662| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23742 Z= 0.212 Angle : 0.742 14.131 32586 Z= 0.359 Chirality : 0.046 0.404 4058 Planarity : 0.005 0.055 3813 Dihedral : 7.352 59.854 6366 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.74 % Favored : 93.87 % Rotamer: Outliers : 2.16 % Allowed : 13.03 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2595 helix: 1.25 (0.24), residues: 468 sheet: -0.05 (0.19), residues: 690 loop : -1.71 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 52 HIS 0.006 0.001 HIS E 364 PHE 0.019 0.002 PHE G 35 TYR 0.025 0.002 TYR K 91 ARG 0.005 0.001 ARG F 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 75) link_NAG-ASN : angle 2.47490 ( 225) link_ALPHA1-6 : bond 0.00743 ( 12) link_ALPHA1-6 : angle 1.96855 ( 36) link_BETA1-4 : bond 0.00441 ( 55) link_BETA1-4 : angle 1.50788 ( 165) link_ALPHA1-2 : bond 0.00389 ( 9) link_ALPHA1-2 : angle 1.65581 ( 27) link_ALPHA1-3 : bond 0.00791 ( 12) link_ALPHA1-3 : angle 2.14542 ( 36) hydrogen bonds : bond 0.04639 ( 782) hydrogen bonds : angle 5.21870 ( 2049) link_BETA1-6 : bond 0.00484 ( 12) link_BETA1-6 : angle 1.29755 ( 36) SS BOND : bond 0.00474 ( 33) SS BOND : angle 0.89259 ( 66) covalent geometry : bond 0.00494 (23534) covalent geometry : angle 0.70060 (31995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7628 (t0) cc_final: 0.7226 (m-40) REVERT: A 391 MET cc_start: 0.8129 (ttp) cc_final: 0.7863 (ttt) REVERT: B 545 MET cc_start: 0.8702 (mmm) cc_final: 0.8153 (tpp) REVERT: B 616 ARG cc_start: 0.5734 (ttm-80) cc_final: 0.3899 (ttm-80) REVERT: H 27 ASP cc_start: 0.7805 (t0) cc_final: 0.7563 (t0) REVERT: H 67 ILE cc_start: 0.8968 (tt) cc_final: 0.8724 (tp) REVERT: L 91 TYR cc_start: 0.8613 (p90) cc_final: 0.7998 (p90) REVERT: C 404 MET cc_start: 0.7369 (mmm) cc_final: 0.6991 (mmm) REVERT: C 497 TYR cc_start: 0.9130 (m-80) cc_final: 0.8362 (m-10) REVERT: D 556 SER cc_start: 0.9004 (m) cc_final: 0.8359 (t) REVERT: D 571 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7405 (tt) REVERT: D 629 SER cc_start: 0.8002 (OUTLIER) cc_final: 0.7345 (t) REVERT: I 79 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7512 (tm-30) REVERT: I 87 TYR cc_start: 0.8553 (m-80) cc_final: 0.8152 (m-10) REVERT: E 391 MET cc_start: 0.8442 (ttp) cc_final: 0.7992 (ttp) REVERT: E 483 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8843 (t) REVERT: F 668 MET cc_start: 0.8394 (mmm) cc_final: 0.7971 (mmp) outliers start: 50 outliers final: 41 residues processed: 267 average time/residue: 0.3506 time to fit residues: 147.8580 Evaluate side-chains 262 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 49 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 253 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082232 restraints weight = 51750.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082784 restraints weight = 39617.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083408 restraints weight = 42897.903| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23742 Z= 0.137 Angle : 0.698 15.384 32586 Z= 0.335 Chirality : 0.045 0.399 4058 Planarity : 0.004 0.050 3813 Dihedral : 6.881 59.722 6366 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.39 % Favored : 94.26 % Rotamer: Outliers : 1.73 % Allowed : 13.68 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2595 helix: 1.23 (0.24), residues: 475 sheet: -0.05 (0.19), residues: 696 loop : -1.67 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 52 HIS 0.003 0.001 HIS E 364 PHE 0.014 0.002 PHE L 94 TYR 0.031 0.001 TYR I 91 ARG 0.004 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 75) link_NAG-ASN : angle 2.34919 ( 225) link_ALPHA1-6 : bond 0.00719 ( 12) link_ALPHA1-6 : angle 1.83476 ( 36) link_BETA1-4 : bond 0.00476 ( 55) link_BETA1-4 : angle 1.43286 ( 165) link_ALPHA1-2 : bond 0.00418 ( 9) link_ALPHA1-2 : angle 1.57077 ( 27) link_ALPHA1-3 : bond 0.00889 ( 12) link_ALPHA1-3 : angle 1.92303 ( 36) hydrogen bonds : bond 0.04288 ( 782) hydrogen bonds : angle 5.12437 ( 2049) link_BETA1-6 : bond 0.00567 ( 12) link_BETA1-6 : angle 1.25558 ( 36) SS BOND : bond 0.00304 ( 33) SS BOND : angle 0.74309 ( 66) covalent geometry : bond 0.00306 (23534) covalent geometry : angle 0.65885 (31995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7622 (t0) cc_final: 0.7166 (m-40) REVERT: A 391 MET cc_start: 0.8068 (ttp) cc_final: 0.7750 (ttt) REVERT: B 545 MET cc_start: 0.8707 (mmm) cc_final: 0.8085 (tpp) REVERT: H 27 ASP cc_start: 0.7713 (t0) cc_final: 0.7441 (t0) REVERT: H 67 ILE cc_start: 0.8967 (tt) cc_final: 0.8729 (tp) REVERT: L 91 TYR cc_start: 0.8493 (p90) cc_final: 0.7909 (p90) REVERT: C 404 MET cc_start: 0.7042 (mmm) cc_final: 0.6832 (mmm) REVERT: C 497 TYR cc_start: 0.9062 (m-80) cc_final: 0.8365 (m-10) REVERT: D 556 SER cc_start: 0.8982 (m) cc_final: 0.8340 (t) REVERT: D 571 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7419 (tt) REVERT: D 629 SER cc_start: 0.8010 (OUTLIER) cc_final: 0.7440 (t) REVERT: I 79 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7335 (tm-30) REVERT: I 87 TYR cc_start: 0.8501 (m-80) cc_final: 0.8134 (m-10) REVERT: E 309 MET cc_start: 0.8758 (tpp) cc_final: 0.8411 (ttm) REVERT: E 391 MET cc_start: 0.8451 (ttp) cc_final: 0.8138 (ttt) REVERT: F 668 MET cc_start: 0.8337 (mmm) cc_final: 0.7985 (mmp) REVERT: J 75 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8266 (tptp) outliers start: 40 outliers final: 35 residues processed: 260 average time/residue: 0.3600 time to fit residues: 149.0732 Evaluate side-chains 257 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 98 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS ** D 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.102426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078626 restraints weight = 52582.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080017 restraints weight = 41948.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080506 restraints weight = 42481.289| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 23742 Z= 0.240 Angle : 0.770 13.071 32586 Z= 0.373 Chirality : 0.047 0.399 4058 Planarity : 0.005 0.055 3813 Dihedral : 7.005 58.969 6366 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.13 % Favored : 92.49 % Rotamer: Outliers : 1.90 % Allowed : 13.90 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2595 helix: 1.17 (0.24), residues: 468 sheet: -0.20 (0.20), residues: 699 loop : -1.84 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 52 HIS 0.007 0.001 HIS E 364 PHE 0.018 0.002 PHE B 537 TYR 0.034 0.002 TYR I 91 ARG 0.010 0.001 ARG G 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 75) link_NAG-ASN : angle 2.43960 ( 225) link_ALPHA1-6 : bond 0.00648 ( 12) link_ALPHA1-6 : angle 1.94266 ( 36) link_BETA1-4 : bond 0.00429 ( 55) link_BETA1-4 : angle 1.54778 ( 165) link_ALPHA1-2 : bond 0.00362 ( 9) link_ALPHA1-2 : angle 1.68288 ( 27) link_ALPHA1-3 : bond 0.00675 ( 12) link_ALPHA1-3 : angle 2.24203 ( 36) hydrogen bonds : bond 0.04761 ( 782) hydrogen bonds : angle 5.28665 ( 2049) link_BETA1-6 : bond 0.00432 ( 12) link_BETA1-6 : angle 1.33844 ( 36) SS BOND : bond 0.00541 ( 33) SS BOND : angle 0.98102 ( 66) covalent geometry : bond 0.00561 (23534) covalent geometry : angle 0.72994 (31995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6640.32 seconds wall clock time: 119 minutes 58.97 seconds (7198.97 seconds total)