Starting phenix.real_space_refine on Thu Mar 5 14:34:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4g_25676/03_2026/7t4g_25676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4g_25676/03_2026/7t4g_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 { model { file = "/net/cci-nas-00/data/ceres_data/7t4g_25676/03_2026/7t4g_25676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4g_25676/03_2026/7t4g_25676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t4g_25676/03_2026/7t4g_25676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4g_25676/03_2026/7t4g_25676.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.67, per 1000 atoms: 0.29 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: 3.01 Conformation dependent library (CDL) restraints added in 1.2 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: 1.12 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: 5.30 Time building geometry restraints manager: 3.73 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.720 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (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 ARG 0.012 0.001 ARG C 231 TYR 0.055 0.008 TYR H 91 PHE 0.039 0.007 PHE B 537 TRP 0.052 0.008 TRP F 586 HIS 0.008 0.003 HIS G 100N Details of bonding type rmsd covalent geometry : bond 0.02216 (23534) covalent geometry : angle 1.83076 (31995) SS BOND : bond 0.06220 ( 33) SS BOND : angle 2.79276 ( 66) hydrogen bonds : bond 0.19221 ( 782) hydrogen bonds : angle 7.27097 ( 2049) 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) 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_BETA1-6 : bond 0.05746 ( 12) link_BETA1-6 : angle 3.31251 ( 36) link_NAG-ASN : bond 0.07541 ( 75) link_NAG-ASN : angle 3.14362 ( 225) *********************** 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 : 0.895 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 163 GLU cc_start: 0.7552 (tp30) cc_final: 0.7233 (tp30) REVERT: A 391 MET cc_start: 0.8515 (ttp) cc_final: 0.8128 (ttm) REVERT: B 545 MET cc_start: 0.7810 (mmm) cc_final: 0.7173 (tpt) REVERT: B 592 GLN cc_start: 0.6083 (tp40) cc_final: 0.5631 (tm-30) REVERT: H 55 ASP cc_start: 0.8567 (m-30) cc_final: 0.8284 (p0) REVERT: H 60 ASN cc_start: 0.8382 (t0) cc_final: 0.8155 (t0) REVERT: H 69 ILE cc_start: 0.8910 (mt) cc_final: 0.8542 (mt) REVERT: L 101 THR cc_start: 0.7782 (p) cc_final: 0.7365 (t) REVERT: C 48 ASN cc_start: 0.8024 (t0) cc_final: 0.7770 (p0) REVERT: C 265 ARG cc_start: 0.8806 (ptp90) cc_final: 0.8021 (ptp-170) REVERT: D 559 LEU cc_start: 0.8780 (tp) cc_final: 0.8425 (tt) 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: 0.8437 (m-30) REVERT: G 90 TYR cc_start: 0.7696 (m-80) cc_final: 0.7441 (m-80) REVERT: I 19 VAL cc_start: 0.6728 (t) cc_final: 0.6518 (p) REVERT: I 37 GLN cc_start: 0.8556 (tt0) cc_final: 0.8305 (tm-30) REVERT: I 74 THR cc_start: 0.7341 (m) cc_final: 0.6704 (p) REVERT: I 79 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6929 (tm-30) REVERT: I 87 TYR cc_start: 0.8943 (m-80) cc_final: 0.8621 (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: 0.8583 (ttt) REVERT: F 557 ARG cc_start: 0.7724 (ptt180) cc_final: 0.7374 (ptt90) REVERT: F 588 THR cc_start: 0.7428 (m) cc_final: 0.7157 (p) REVERT: F 633 LYS cc_start: 0.7977 (mttp) cc_final: 0.7770 (mmtt) REVERT: F 668 MET cc_start: 0.8797 (mmm) cc_final: 0.8542 (mmp) REVERT: J 54 ASN cc_start: 0.8052 (t0) cc_final: 0.7799 (p0) REVERT: J 91 TYR cc_start: 0.8017 (m-80) cc_final: 0.7673 (m-10) REVERT: J 100 TYR cc_start: 0.8719 (m-80) cc_final: 0.8466 (m-80) REVERT: K 4 LEU cc_start: 0.8586 (tp) cc_final: 0.8366 (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: 0.7542 (mtt-85) outliers start: 6 outliers final: 2 residues processed: 585 average time/residue: 0.1961 time to fit residues: 170.4228 Evaluate side-chains 289 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 566 GLN B 635 ASN B 661 GLN B 672 GLN 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 G 5 GLN G 76 ASN G 77 GLN I 6 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN E 223 HIS ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 HIS E 433 HIS ** F 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088514 restraints weight = 51356.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087717 restraints weight = 45522.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089031 restraints weight = 42055.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089411 restraints weight = 31973.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.089625 restraints weight = 30123.668| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23742 Z= 0.188 Angle : 0.879 13.732 32586 Z= 0.427 Chirality : 0.051 0.517 4058 Planarity : 0.005 0.055 3813 Dihedral : 11.680 86.587 6368 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.93 % Favored : 95.61 % Rotamer: Outliers : 2.29 % Allowed : 8.14 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2595 helix: 1.20 (0.24), residues: 447 sheet: 0.46 (0.20), residues: 627 loop : -0.63 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 49 TYR 0.028 0.002 TYR L 91 PHE 0.021 0.002 PHE B 537 TRP 0.021 0.002 TRP J 36 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00396 (23534) covalent geometry : angle 0.81571 (31995) SS BOND : bond 0.00365 ( 33) SS BOND : angle 1.01333 ( 66) hydrogen bonds : bond 0.06393 ( 782) hydrogen bonds : angle 6.00659 ( 2049) link_ALPHA1-2 : bond 0.00415 ( 9) link_ALPHA1-2 : angle 2.18791 ( 27) link_ALPHA1-3 : bond 0.00946 ( 12) link_ALPHA1-3 : angle 2.39408 ( 36) link_ALPHA1-6 : bond 0.00795 ( 12) link_ALPHA1-6 : angle 1.63655 ( 36) link_BETA1-4 : bond 0.00698 ( 55) link_BETA1-4 : angle 2.53889 ( 165) link_BETA1-6 : bond 0.00869 ( 12) link_BETA1-6 : angle 1.29901 ( 36) link_NAG-ASN : bond 0.00714 ( 75) link_NAG-ASN : angle 3.15356 ( 225) *********************** 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 400 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7298 (t0) cc_final: 0.6827 (m-40) REVERT: A 391 MET cc_start: 0.8037 (ttp) cc_final: 0.7676 (ttt) REVERT: B 629 SER cc_start: 0.8044 (m) cc_final: 0.7665 (t) REVERT: B 668 MET cc_start: 0.8115 (mmm) cc_final: 0.7763 (tpt) REVERT: H 43 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8341 (mmtm) REVERT: L 36 TYR cc_start: 0.8512 (m-80) cc_final: 0.8159 (m-80) REVERT: L 48 ILE cc_start: 0.8625 (mm) cc_final: 0.8402 (mt) REVERT: C 232 TYR cc_start: 0.8061 (m-80) cc_final: 0.7777 (m-80) REVERT: D 559 LEU cc_start: 0.8593 (tp) cc_final: 0.8328 (tt) REVERT: D 620 CYS cc_start: 0.7261 (m) cc_final: 0.7032 (p) REVERT: D 631 ILE cc_start: 0.8931 (mm) cc_final: 0.8696 (pt) REVERT: I 87 TYR cc_start: 0.8607 (m-80) cc_final: 0.8379 (m-80) REVERT: E 391 MET cc_start: 0.8295 (ttp) cc_final: 0.7996 (ttt) REVERT: F 556 SER cc_start: 0.7185 (t) cc_final: 0.6736 (p) REVERT: F 633 LYS cc_start: 0.7573 (mttp) cc_final: 0.7369 (mmtt) REVERT: F 668 MET cc_start: 0.8629 (mmm) cc_final: 0.8388 (mmt) REVERT: J 75 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8201 (tptp) REVERT: K 24 ARG cc_start: 0.7376 (mmm-85) cc_final: 0.7082 (mtm-85) outliers start: 53 outliers final: 24 residues processed: 382 average time/residue: 0.1721 time to fit residues: 101.9272 Evaluate side-chains 280 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 394 ASN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 11 LEU 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 154 optimal weight: 9.9990 chunk 201 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 635 ASN H 77 GLN L 79 GLN C 394 ASN G 56 ASN I 79 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN E 336 ASN J 100NHIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085680 restraints weight = 51803.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085814 restraints weight = 40603.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086801 restraints weight = 40909.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087133 restraints weight = 31965.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.087423 restraints weight = 29705.173| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3511 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= 0.175 Angle : 0.770 10.889 32586 Z= 0.377 Chirality : 0.047 0.437 4058 Planarity : 0.004 0.045 3813 Dihedral : 9.784 78.986 6368 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.35 % Favored : 95.18 % Rotamer: Outliers : 2.47 % Allowed : 9.57 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2595 helix: 1.05 (0.24), residues: 475 sheet: 0.30 (0.19), residues: 714 loop : -0.97 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 13 TYR 0.028 0.002 TYR K 91 PHE 0.021 0.002 PHE L 62 TRP 0.020 0.002 TRP C 52 HIS 0.004 0.001 HIS J 100N Details of bonding type rmsd covalent geometry : bond 0.00389 (23534) covalent geometry : angle 0.72137 (31995) SS BOND : bond 0.00491 ( 33) SS BOND : angle 1.12100 ( 66) hydrogen bonds : bond 0.05434 ( 782) hydrogen bonds : angle 5.52263 ( 2049) link_ALPHA1-2 : bond 0.00483 ( 9) link_ALPHA1-2 : angle 1.73141 ( 27) link_ALPHA1-3 : bond 0.00984 ( 12) link_ALPHA1-3 : angle 1.84004 ( 36) link_ALPHA1-6 : bond 0.00787 ( 12) link_ALPHA1-6 : angle 1.80014 ( 36) link_BETA1-4 : bond 0.00605 ( 55) link_BETA1-4 : angle 1.90390 ( 165) link_BETA1-6 : bond 0.00644 ( 12) link_BETA1-6 : angle 1.32530 ( 36) link_NAG-ASN : bond 0.00460 ( 75) link_NAG-ASN : angle 2.66316 ( 225) *********************** 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 348 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 291 time to evaluate : 0.882 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: 0.7322 (t0) cc_final: 0.6878 (m-40) REVERT: A 391 MET cc_start: 0.8177 (ttp) cc_final: 0.7838 (ttt) REVERT: B 668 MET cc_start: 0.8153 (mmm) cc_final: 0.7931 (tpt) REVERT: H 43 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8419 (mmtm) REVERT: L 36 TYR cc_start: 0.8611 (m-80) cc_final: 0.8365 (m-80) REVERT: C 309 MET cc_start: 0.8823 (ttp) cc_final: 0.8496 (ttp) REVERT: D 556 SER cc_start: 0.8826 (m) cc_final: 0.8178 (t) REVERT: D 559 LEU cc_start: 0.8684 (tp) cc_final: 0.8425 (tt) REVERT: I 55 GLN cc_start: 0.7980 (tp40) cc_final: 0.7729 (tp-100) REVERT: I 82 ASP cc_start: 0.7440 (m-30) cc_final: 0.7048 (m-30) REVERT: E 391 MET cc_start: 0.8302 (ttp) cc_final: 0.8005 (ttt) REVERT: F 633 LYS cc_start: 0.7655 (mttp) cc_final: 0.7426 (mmtt) REVERT: F 668 MET cc_start: 0.8585 (mmm) cc_final: 0.8251 (mmt) REVERT: K 24 ARG cc_start: 0.7486 (mmm-85) cc_final: 0.7144 (mtm-85) outliers start: 57 outliers final: 37 residues processed: 324 average time/residue: 0.1636 time to fit residues: 83.1246 Evaluate side-chains 285 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 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 L residue 105 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 107 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 G residue 25 SER Chi-restraints excluded: chain G residue 28 THR 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 11 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 67 MET 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 181 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 635 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 394 ASN ** 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 = 0.3706 r_free = 0.3706 target = 0.106155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082469 restraints weight = 51887.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082940 restraints weight = 42013.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083400 restraints weight = 40930.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084581 restraints weight = 33846.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084577 restraints weight = 29067.331| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23742 Z= 0.203 Angle : 0.757 10.114 32586 Z= 0.368 Chirality : 0.047 0.424 4058 Planarity : 0.005 0.054 3813 Dihedral : 8.573 72.419 6366 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.97 % Favored : 94.57 % Rotamer: Outliers : 2.60 % Allowed : 10.61 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2595 helix: 1.13 (0.24), residues: 475 sheet: 0.16 (0.19), residues: 720 loop : -1.25 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 594 TYR 0.028 0.002 TYR K 91 PHE 0.022 0.002 PHE E 346 TRP 0.025 0.002 TRP D 586 HIS 0.005 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00467 (23534) covalent geometry : angle 0.71361 (31995) SS BOND : bond 0.00441 ( 33) SS BOND : angle 0.95551 ( 66) hydrogen bonds : bond 0.05005 ( 782) hydrogen bonds : angle 5.33951 ( 2049) link_ALPHA1-2 : bond 0.00391 ( 9) link_ALPHA1-2 : angle 1.73821 ( 27) link_ALPHA1-3 : bond 0.00780 ( 12) link_ALPHA1-3 : angle 2.20395 ( 36) link_ALPHA1-6 : bond 0.00813 ( 12) link_ALPHA1-6 : angle 2.02874 ( 36) link_BETA1-4 : bond 0.00445 ( 55) link_BETA1-4 : angle 1.74080 ( 165) link_BETA1-6 : bond 0.00566 ( 12) link_BETA1-6 : angle 1.28932 ( 36) link_NAG-ASN : bond 0.00401 ( 75) link_NAG-ASN : angle 2.43842 ( 225) *********************** 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 330 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 270 time to evaluate : 0.833 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: 0.7408 (t0) cc_final: 0.7027 (m-40) REVERT: A 391 MET cc_start: 0.8284 (ttp) cc_final: 0.7924 (ttt) REVERT: B 545 MET cc_start: 0.8373 (mmm) cc_final: 0.7128 (mtp) REVERT: B 600 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8735 (mtpp) REVERT: D 556 SER cc_start: 0.8846 (m) cc_final: 0.8162 (t) REVERT: D 629 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7321 (t) REVERT: I 58 VAL cc_start: 0.8618 (t) cc_final: 0.8227 (p) REVERT: E 172 MET cc_start: 0.7767 (tpt) cc_final: 0.7565 (tpt) REVERT: E 391 MET cc_start: 0.8409 (ttp) cc_final: 0.8135 (ttt) REVERT: E 483 SER cc_start: 0.9018 (t) cc_final: 0.8774 (t) REVERT: F 668 MET cc_start: 0.8539 (mmm) cc_final: 0.8201 (mmp) REVERT: K 24 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7267 (mtt180) outliers start: 60 outliers final: 40 residues processed: 306 average time/residue: 0.1686 time to fit residues: 80.6684 Evaluate side-chains 273 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 571 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 D residue 534 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain I residue 3 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 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 598 ILE Chi-restraints excluded: chain F residue 621 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 231 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 270 GLN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 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** K 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.107863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084875 restraints weight = 51413.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084789 restraints weight = 39772.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085808 restraints weight = 41622.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086208 restraints weight = 31302.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086485 restraints weight = 29394.475| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23742 Z= 0.130 Angle : 0.690 9.772 32586 Z= 0.332 Chirality : 0.045 0.400 4058 Planarity : 0.004 0.047 3813 Dihedral : 7.882 66.634 6366 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.82 % Favored : 94.76 % Rotamer: Outliers : 2.38 % Allowed : 11.77 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2595 helix: 1.35 (0.24), residues: 474 sheet: 0.22 (0.19), residues: 732 loop : -1.27 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 594 TYR 0.029 0.001 TYR K 91 PHE 0.022 0.002 PHE D 537 TRP 0.022 0.001 TRP E 345 HIS 0.003 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00279 (23534) covalent geometry : angle 0.65089 (31995) SS BOND : bond 0.00274 ( 33) SS BOND : angle 0.72412 ( 66) hydrogen bonds : bond 0.04447 ( 782) hydrogen bonds : angle 5.15439 ( 2049) link_ALPHA1-2 : bond 0.00440 ( 9) link_ALPHA1-2 : angle 1.57157 ( 27) link_ALPHA1-3 : bond 0.01002 ( 12) link_ALPHA1-3 : angle 1.90836 ( 36) link_ALPHA1-6 : bond 0.00927 ( 12) link_ALPHA1-6 : angle 1.99344 ( 36) link_BETA1-4 : bond 0.00525 ( 55) link_BETA1-4 : angle 1.50710 ( 165) link_BETA1-6 : bond 0.00643 ( 12) link_BETA1-6 : angle 1.26421 ( 36) link_NAG-ASN : bond 0.00367 ( 75) link_NAG-ASN : angle 2.24249 ( 225) *********************** 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 320 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 265 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7361 (t0) cc_final: 0.6969 (m-40) REVERT: A 391 MET cc_start: 0.8200 (ttp) cc_final: 0.7877 (ttt) REVERT: B 600 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8674 (mtpp) REVERT: B 669 TYR cc_start: 0.7718 (t80) cc_final: 0.7318 (t80) REVERT: L 18 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7264 (mmm-85) REVERT: D 556 SER cc_start: 0.8701 (m) cc_final: 0.8058 (t) REVERT: D 571 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7258 (tt) REVERT: D 603 LYS cc_start: 0.8823 (tppt) cc_final: 0.8532 (tppt) REVERT: D 629 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7330 (t) REVERT: I 55 GLN cc_start: 0.7807 (tp40) cc_final: 0.7547 (tp-100) REVERT: I 58 VAL cc_start: 0.8522 (t) cc_final: 0.8305 (p) REVERT: E 391 MET cc_start: 0.8369 (ttp) cc_final: 0.8038 (ttt) REVERT: F 552 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.5221 (pt) REVERT: F 668 MET cc_start: 0.8498 (mmm) cc_final: 0.8139 (mmp) outliers start: 55 outliers final: 36 residues processed: 300 average time/residue: 0.1789 time to fit residues: 82.6054 Evaluate side-chains 270 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 571 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 647 ASP 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 C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 57 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 210 HIS Chi-restraints excluded: chain E residue 345 TRP 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 552 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 11 VAL Chi-restraints excluded: chain J residue 35 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 104 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 270 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 HIS ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 6 GLN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.078956 restraints weight = 52536.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080422 restraints weight = 42785.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.080963 restraints weight = 38585.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081258 restraints weight = 30377.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081685 restraints weight = 28215.461| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 23742 Z= 0.321 Angle : 0.841 10.158 32586 Z= 0.409 Chirality : 0.049 0.424 4058 Planarity : 0.005 0.056 3813 Dihedral : 8.247 68.231 6366 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.01 % Favored : 93.56 % Rotamer: Outliers : 2.77 % Allowed : 12.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.16), residues: 2595 helix: 1.12 (0.24), residues: 466 sheet: -0.03 (0.19), residues: 708 loop : -1.68 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 366 TYR 0.031 0.003 TYR C 401 PHE 0.030 0.003 PHE E 346 TRP 0.022 0.002 TRP D 625 HIS 0.008 0.002 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00750 (23534) covalent geometry : angle 0.80331 (31995) SS BOND : bond 0.00756 ( 33) SS BOND : angle 1.19484 ( 66) hydrogen bonds : bond 0.05232 ( 782) hydrogen bonds : angle 5.40375 ( 2049) link_ALPHA1-2 : bond 0.00458 ( 9) link_ALPHA1-2 : angle 1.76751 ( 27) link_ALPHA1-3 : bond 0.00659 ( 12) link_ALPHA1-3 : angle 2.37014 ( 36) link_ALPHA1-6 : bond 0.00773 ( 12) link_ALPHA1-6 : angle 2.17862 ( 36) link_BETA1-4 : bond 0.00450 ( 55) link_BETA1-4 : angle 1.66284 ( 165) link_BETA1-6 : bond 0.00449 ( 12) link_BETA1-6 : angle 1.35468 ( 36) link_NAG-ASN : bond 0.00480 ( 75) link_NAG-ASN : angle 2.43327 ( 225) *********************** 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 299 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7464 (t0) cc_final: 0.7076 (m-40) REVERT: A 391 MET cc_start: 0.8431 (ttp) cc_final: 0.8145 (ttt) REVERT: B 545 MET cc_start: 0.8610 (mmm) cc_final: 0.8055 (tpp) REVERT: H 27 ASP cc_start: 0.7599 (t0) cc_final: 0.7313 (t0) REVERT: H 77 GLN cc_start: 0.7744 (mp-120) cc_final: 0.7005 (mp10) REVERT: L 18 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7597 (mmm-85) REVERT: D 556 SER cc_start: 0.9043 (m) cc_final: 0.8399 (t) REVERT: D 603 LYS cc_start: 0.8838 (tppt) cc_final: 0.8369 (tptp) REVERT: D 629 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7368 (t) REVERT: E 391 MET cc_start: 0.8575 (ttp) cc_final: 0.8269 (ttt) REVERT: F 633 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7998 (mmtp) REVERT: F 668 MET cc_start: 0.8537 (mmm) cc_final: 0.8088 (mmp) outliers start: 64 outliers final: 50 residues processed: 272 average time/residue: 0.1670 time to fit residues: 71.6399 Evaluate side-chains 275 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 647 ASP 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 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 318 THR Chi-restraints excluded: chain C residue 335 ILE 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 629 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 55 ASP 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 74 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 318 THR 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 598 ILE Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 236 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 270 GLN L 90 GLN C 425 HIS ** 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 = 0.3671 r_free = 0.3671 target = 0.103915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080182 restraints weight = 52056.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081766 restraints weight = 41427.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082119 restraints weight = 39866.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082385 restraints weight = 30276.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082840 restraints weight = 27724.110| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 23742 Z= 0.211 Angle : 0.755 14.272 32586 Z= 0.363 Chirality : 0.047 0.430 4058 Planarity : 0.004 0.052 3813 Dihedral : 7.988 65.026 6366 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.78 % Favored : 93.80 % Rotamer: Outliers : 2.73 % Allowed : 13.20 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.16), residues: 2595 helix: 1.18 (0.24), residues: 466 sheet: -0.01 (0.19), residues: 687 loop : -1.69 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 594 TYR 0.028 0.002 TYR K 91 PHE 0.025 0.002 PHE F 537 TRP 0.019 0.002 TRP C 121 HIS 0.005 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00488 (23534) covalent geometry : angle 0.71286 (31995) SS BOND : bond 0.00447 ( 33) SS BOND : angle 0.95520 ( 66) hydrogen bonds : bond 0.04775 ( 782) hydrogen bonds : angle 5.30056 ( 2049) link_ALPHA1-2 : bond 0.00427 ( 9) link_ALPHA1-2 : angle 1.67068 ( 27) link_ALPHA1-3 : bond 0.00870 ( 12) link_ALPHA1-3 : angle 2.11787 ( 36) link_ALPHA1-6 : bond 0.00792 ( 12) link_ALPHA1-6 : angle 2.00494 ( 36) link_BETA1-4 : bond 0.00447 ( 55) link_BETA1-4 : angle 1.50994 ( 165) link_BETA1-6 : bond 0.00511 ( 12) link_BETA1-6 : angle 1.29491 ( 36) link_NAG-ASN : bond 0.00433 ( 75) link_NAG-ASN : angle 2.54439 ( 225) *********************** 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 296 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 0.862 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: 0.7577 (t0) cc_final: 0.7218 (m-40) REVERT: A 391 MET cc_start: 0.8182 (ttp) cc_final: 0.7784 (ttt) REVERT: B 545 MET cc_start: 0.8623 (mmm) cc_final: 0.8103 (tpp) REVERT: H 27 ASP cc_start: 0.7682 (t0) cc_final: 0.7383 (t0) REVERT: H 67 ILE cc_start: 0.9057 (tt) cc_final: 0.8857 (tp) REVERT: H 77 GLN cc_start: 0.7631 (mp-120) cc_final: 0.7394 (mp10) REVERT: H 89 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7978 (pp) REVERT: D 556 SER cc_start: 0.8979 (m) cc_final: 0.8325 (t) REVERT: D 603 LYS cc_start: 0.8830 (tppt) cc_final: 0.8319 (tptp) REVERT: D 629 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7472 (t) REVERT: D 668 MET cc_start: 0.6272 (mtm) cc_final: 0.5569 (tpt) REVERT: E 391 MET cc_start: 0.8524 (ttp) cc_final: 0.8230 (ttt) REVERT: E 483 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8882 (t) REVERT: F 633 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8044 (mmtp) REVERT: F 668 MET cc_start: 0.8505 (mmm) cc_final: 0.8059 (mmp) REVERT: J 91 TYR cc_start: 0.7657 (m-10) cc_final: 0.7435 (m-10) REVERT: K 3 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (pp) outliers start: 63 outliers final: 43 residues processed: 274 average time/residue: 0.1619 time to fit residues: 70.7629 Evaluate side-chains 270 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 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 H residue 65 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain L residue 3 LEU 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 335 ILE Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 391 MET 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 25 SER Chi-restraints excluded: chain G residue 28 THR 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 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 107 LEU 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 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 163 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 219 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** F 566 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 = 0.3650 r_free = 0.3650 target = 0.103163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079479 restraints weight = 52131.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079399 restraints weight = 43611.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079807 restraints weight = 47394.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081349 restraints weight = 37078.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081386 restraints weight = 29444.562| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4994 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= 0.193 Angle : 0.746 16.844 32586 Z= 0.358 Chirality : 0.047 0.418 4058 Planarity : 0.004 0.053 3813 Dihedral : 7.567 62.166 6366 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.36 % Favored : 93.26 % Rotamer: Outliers : 2.47 % Allowed : 13.64 % Favored : 83.90 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2595 helix: 1.19 (0.24), residues: 466 sheet: -0.09 (0.19), residues: 690 loop : -1.75 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 94 TYR 0.028 0.002 TYR K 91 PHE 0.023 0.002 PHE D 537 TRP 0.020 0.001 TRP C 121 HIS 0.005 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00442 (23534) covalent geometry : angle 0.70257 (31995) SS BOND : bond 0.00424 ( 33) SS BOND : angle 0.89929 ( 66) hydrogen bonds : bond 0.04598 ( 782) hydrogen bonds : angle 5.21962 ( 2049) link_ALPHA1-2 : bond 0.00397 ( 9) link_ALPHA1-2 : angle 1.66831 ( 27) link_ALPHA1-3 : bond 0.00731 ( 12) link_ALPHA1-3 : angle 2.08758 ( 36) link_ALPHA1-6 : bond 0.00773 ( 12) link_ALPHA1-6 : angle 2.04494 ( 36) link_BETA1-4 : bond 0.00445 ( 55) link_BETA1-4 : angle 1.49857 ( 165) link_BETA1-6 : bond 0.00515 ( 12) link_BETA1-6 : angle 1.28947 ( 36) link_NAG-ASN : bond 0.00732 ( 75) link_NAG-ASN : angle 2.56748 ( 225) *********************** 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 293 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.887 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: 0.7547 (t0) cc_final: 0.7223 (m-40) REVERT: A 309 MET cc_start: 0.7905 (tpt) cc_final: 0.7647 (mmm) REVERT: A 391 MET cc_start: 0.8150 (ttp) cc_final: 0.7796 (ttt) REVERT: B 545 MET cc_start: 0.8626 (mmm) cc_final: 0.8089 (tpp) REVERT: H 27 ASP cc_start: 0.7735 (t0) cc_final: 0.7396 (t0) REVERT: H 77 GLN cc_start: 0.7575 (mp-120) cc_final: 0.7358 (mp10) REVERT: H 89 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7884 (pp) REVERT: C 266 MET cc_start: 0.8639 (mmm) cc_final: 0.8306 (tpt) REVERT: C 497 TYR cc_start: 0.9135 (m-80) cc_final: 0.8371 (m-10) REVERT: D 556 SER cc_start: 0.8912 (m) cc_final: 0.8283 (t) REVERT: D 571 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7411 (tt) REVERT: D 629 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7348 (t) REVERT: E 391 MET cc_start: 0.8490 (ttp) cc_final: 0.8212 (ttt) REVERT: E 483 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8834 (t) REVERT: F 668 MET cc_start: 0.8505 (mmm) cc_final: 0.8026 (mmp) outliers start: 57 outliers final: 40 residues processed: 275 average time/residue: 0.1684 time to fit residues: 73.8068 Evaluate side-chains 264 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 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 H residue 89 ILE Chi-restraints excluded: chain L residue 3 LEU 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 335 ILE Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 391 MET 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 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 55 ASP 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 74 SER Chi-restraints excluded: chain E residue 107 LEU 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 586 TRP Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 75 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 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 ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** F 566 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 = 0.3657 r_free = 0.3657 target = 0.103620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079869 restraints weight = 52379.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080393 restraints weight = 44179.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080731 restraints weight = 43256.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082015 restraints weight = 34704.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082004 restraints weight = 28839.795| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23742 Z= 0.174 Angle : 0.738 19.020 32586 Z= 0.351 Chirality : 0.046 0.410 4058 Planarity : 0.004 0.054 3813 Dihedral : 7.310 59.318 6366 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.01 % Favored : 93.64 % Rotamer: Outliers : 2.12 % Allowed : 13.94 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2595 helix: 1.21 (0.24), residues: 466 sheet: -0.12 (0.19), residues: 693 loop : -1.74 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 594 TYR 0.028 0.002 TYR K 91 PHE 0.022 0.002 PHE D 537 TRP 0.026 0.001 TRP D 586 HIS 0.004 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00399 (23534) covalent geometry : angle 0.68694 (31995) SS BOND : bond 0.00388 ( 33) SS BOND : angle 0.83584 ( 66) hydrogen bonds : bond 0.04470 ( 782) hydrogen bonds : angle 5.21144 ( 2049) link_ALPHA1-2 : bond 0.00398 ( 9) link_ALPHA1-2 : angle 1.63424 ( 27) link_ALPHA1-3 : bond 0.00850 ( 12) link_ALPHA1-3 : angle 2.04481 ( 36) link_ALPHA1-6 : bond 0.00740 ( 12) link_ALPHA1-6 : angle 1.89629 ( 36) link_BETA1-4 : bond 0.00459 ( 55) link_BETA1-4 : angle 1.46993 ( 165) link_BETA1-6 : bond 0.00524 ( 12) link_BETA1-6 : angle 1.28352 ( 36) link_NAG-ASN : bond 0.00397 ( 75) link_NAG-ASN : angle 2.86398 ( 225) *********************** 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 281 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7536 (t0) cc_final: 0.7233 (m-40) REVERT: A 309 MET cc_start: 0.7982 (tpt) cc_final: 0.7748 (mmm) REVERT: A 391 MET cc_start: 0.8326 (ttp) cc_final: 0.7974 (ttt) REVERT: B 545 MET cc_start: 0.8644 (mmm) cc_final: 0.8087 (tpp) REVERT: H 27 ASP cc_start: 0.7714 (t0) cc_final: 0.7363 (t0) REVERT: H 77 GLN cc_start: 0.7518 (mp-120) cc_final: 0.7303 (mp10) REVERT: H 89 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7914 (pp) REVERT: C 266 MET cc_start: 0.8673 (mmm) cc_final: 0.8221 (tpt) REVERT: C 497 TYR cc_start: 0.9125 (m-80) cc_final: 0.8344 (m-10) REVERT: D 556 SER cc_start: 0.8852 (m) cc_final: 0.8254 (t) REVERT: D 571 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7402 (tt) REVERT: D 629 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7299 (t) REVERT: E 391 MET cc_start: 0.8545 (ttp) cc_final: 0.8209 (ttt) REVERT: E 483 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8839 (t) REVERT: F 668 MET cc_start: 0.8422 (mmm) cc_final: 0.8002 (mmp) outliers start: 49 outliers final: 41 residues processed: 264 average time/residue: 0.1648 time to fit residues: 69.0036 Evaluate side-chains 261 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 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 H residue 89 ILE Chi-restraints excluded: chain L residue 3 LEU 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 335 ILE Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 391 MET 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 55 ASP 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 74 SER Chi-restraints excluded: chain E residue 107 LEU 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 586 TRP Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 63 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 128 optimal weight: 0.0060 chunk 144 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN L 90 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.105443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081237 restraints weight = 51916.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.081885 restraints weight = 41671.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082551 restraints weight = 39700.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082956 restraints weight = 31284.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083309 restraints weight = 28837.251| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23742 Z= 0.134 Angle : 0.709 17.645 32586 Z= 0.339 Chirality : 0.045 0.400 4058 Planarity : 0.004 0.048 3813 Dihedral : 6.875 57.014 6366 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.78 % Favored : 93.91 % Rotamer: Outliers : 1.65 % Allowed : 14.59 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2595 helix: 1.22 (0.24), residues: 472 sheet: -0.19 (0.19), residues: 708 loop : -1.77 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 13 TYR 0.027 0.001 TYR K 91 PHE 0.021 0.002 PHE D 537 TRP 0.023 0.001 TRP H 36 HIS 0.004 0.001 HIS E 291 Details of bonding type rmsd covalent geometry : bond 0.00295 (23534) covalent geometry : angle 0.66412 (31995) SS BOND : bond 0.00300 ( 33) SS BOND : angle 0.76544 ( 66) hydrogen bonds : bond 0.04229 ( 782) hydrogen bonds : angle 5.14898 ( 2049) link_ALPHA1-2 : bond 0.00423 ( 9) link_ALPHA1-2 : angle 1.56272 ( 27) link_ALPHA1-3 : bond 0.00880 ( 12) link_ALPHA1-3 : angle 1.91818 ( 36) link_ALPHA1-6 : bond 0.00722 ( 12) link_ALPHA1-6 : angle 1.81937 ( 36) link_BETA1-4 : bond 0.00481 ( 55) link_BETA1-4 : angle 1.41453 ( 165) link_BETA1-6 : bond 0.00567 ( 12) link_BETA1-6 : angle 1.26796 ( 36) link_NAG-ASN : bond 0.00389 ( 75) link_NAG-ASN : angle 2.61562 ( 225) ********************** 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 269 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.874 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: 0.7756 (t0) cc_final: 0.7343 (m-40) REVERT: A 309 MET cc_start: 0.7944 (tpt) cc_final: 0.7730 (mmm) REVERT: A 391 MET cc_start: 0.8283 (ttp) cc_final: 0.7985 (ttt) REVERT: B 545 MET cc_start: 0.8694 (mmm) cc_final: 0.8329 (tpp) REVERT: H 27 ASP cc_start: 0.7810 (t0) cc_final: 0.7375 (t0) REVERT: H 89 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7940 (pp) REVERT: L 91 TYR cc_start: 0.8380 (p90) cc_final: 0.8153 (p90) REVERT: C 266 MET cc_start: 0.8719 (mmm) cc_final: 0.8334 (tpt) REVERT: C 404 MET cc_start: 0.8058 (mmm) cc_final: 0.7081 (mtp) REVERT: D 556 SER cc_start: 0.8934 (m) cc_final: 0.8289 (t) REVERT: D 571 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7372 (tt) REVERT: D 629 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7581 (t) REVERT: E 391 MET cc_start: 0.8444 (ttp) cc_final: 0.8106 (ttt) REVERT: F 668 MET cc_start: 0.8338 (mmm) cc_final: 0.7931 (mmp) outliers start: 38 outliers final: 32 residues processed: 256 average time/residue: 0.1659 time to fit residues: 67.2314 Evaluate side-chains 253 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 571 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 H residue 89 ILE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 58 VAL 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 11 VAL Chi-restraints excluded: chain G residue 25 SER 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 74 SER Chi-restraints excluded: chain E residue 107 LEU 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 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 136 optimal weight: 9.9990 chunk 225 optimal weight: 0.0050 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 99 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 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 = 0.3698 r_free = 0.3698 target = 0.106178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082914 restraints weight = 51500.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082673 restraints weight = 41284.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083201 restraints weight = 42957.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084604 restraints weight = 34595.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084640 restraints weight = 28622.567| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23742 Z= 0.126 Angle : 0.689 17.241 32586 Z= 0.331 Chirality : 0.044 0.382 4058 Planarity : 0.004 0.048 3813 Dihedral : 6.510 56.053 6366 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.51 % Favored : 94.22 % Rotamer: Outliers : 1.69 % Allowed : 14.85 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2595 helix: 1.28 (0.24), residues: 472 sheet: -0.23 (0.19), residues: 726 loop : -1.70 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.028 0.001 TYR K 91 PHE 0.021 0.002 PHE D 537 TRP 0.023 0.001 TRP E 345 HIS 0.004 0.001 HIS E 291 Details of bonding type rmsd covalent geometry : bond 0.00275 (23534) covalent geometry : angle 0.64561 (31995) SS BOND : bond 0.00284 ( 33) SS BOND : angle 0.72685 ( 66) hydrogen bonds : bond 0.04096 ( 782) hydrogen bonds : angle 5.08050 ( 2049) link_ALPHA1-2 : bond 0.00417 ( 9) link_ALPHA1-2 : angle 1.53716 ( 27) link_ALPHA1-3 : bond 0.00851 ( 12) link_ALPHA1-3 : angle 1.88897 ( 36) link_ALPHA1-6 : bond 0.00694 ( 12) link_ALPHA1-6 : angle 1.73175 ( 36) link_BETA1-4 : bond 0.00479 ( 55) link_BETA1-4 : angle 1.40449 ( 165) link_BETA1-6 : bond 0.00570 ( 12) link_BETA1-6 : angle 1.26895 ( 36) link_NAG-ASN : bond 0.00392 ( 75) link_NAG-ASN : angle 2.51583 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.60 seconds wall clock time: 58 minutes 45.06 seconds (3525.06 seconds total)