Starting phenix.real_space_refine on Thu Jun 19 02:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ulu_42366/06_2025/8ulu_42366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ulu_42366/06_2025/8ulu_42366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ulu_42366/06_2025/8ulu_42366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ulu_42366/06_2025/8ulu_42366.map" model { file = "/net/cci-nas-00/data/ceres_data/8ulu_42366/06_2025/8ulu_42366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ulu_42366/06_2025/8ulu_42366.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 121 5.16 5 C 13816 2.51 5 N 3714 2.21 5 O 4378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22029 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3450 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 982 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3450 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 982 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3446 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 982 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1024 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1024 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1024 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1091 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 791 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 791 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 791 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" 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: "R" 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: "S" 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: "T" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" 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: "g" 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: "h" 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 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: "l" 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: "m" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "q" 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: "r" 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: "s" 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: "t" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: 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 Time building chain proxies: 13.83, per 1000 atoms: 0.63 Number of scatterers: 22029 At special positions: 0 Unit cell: (145.6, 136.448, 161.408, 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 121 16.00 O 4378 8.00 N 3714 7.00 C 13816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 4 " - " MAN m 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA b 3 " - " MAN b 7 " " MAN b 4 " - " MAN b 5 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " BMA p 3 " - " MAN p 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA b 3 " - " MAN b 4 " " MAN b 4 " - " MAN b 6 " " BMA j 3 " - " MAN j 5 " " BMA m 3 " - " MAN m 6 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 448 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 339 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 160 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN C 156 " " NAG b 1 " - " ASN C 160 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 276 " " NAG e 1 " - " ASN C 295 " " NAG f 1 " - " ASN C 301 " " NAG g 1 " - " ASN C 332 " " NAG h 1 " - " ASN C 363 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 197 " " NAG l 1 " - " ASN E 156 " " NAG m 1 " - " ASN E 160 " " NAG n 1 " - " ASN E 197 " " NAG o 1 " - " ASN E 234 " " NAG p 1 " - " ASN E 262 " " NAG q 1 " - " ASN E 276 " " NAG r 1 " - " ASN E 295 " " NAG s 1 " - " ASN E 301 " " NAG t 1 " - " ASN E 332 " " NAG u 1 " - " ASN E 363 " " NAG v 1 " - " ASN E 386 " " NAG w 1 " - " ASN E 448 " Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 2.5 seconds 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4916 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 55 sheets defined 19.4% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.444A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.135A pdb=" N ARG A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.593A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.733A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.593A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 634 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.755A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.683A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.815A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.908A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.164A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.877A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 4.085A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.467A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.842A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 474 through 481 removed outlier: 3.754A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.477A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.834A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.524A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 4.210A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.604A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.997A pdb=" N VAL G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.938A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.849A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.557A pdb=" N ASP J 86 " --> pdb=" O LYS J 83 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.767A pdb=" N VAL M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 499 removed outlier: 5.916A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.838A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.213A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 310 removed outlier: 5.006A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 330 through 334 removed outlier: 3.881A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.554A pdb=" N VAL C 36 " --> pdb=" O VAL D 608 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.862A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.931A pdb=" N CYS C 131 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AB8, first strand: chain 'C' and resid 202 through 203 removed outlier: 8.968A pdb=" N GLN C 432 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET C 426 " --> pdb=" O GLN C 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 4.019A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 452 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 4.019A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 383 through 385 removed outlier: 3.998A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 304 through 309 Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.677A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.636A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.102A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.964A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.842A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.600A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 removed outlier: 3.689A pdb=" N LEU E 452 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 304 through 310 Processing sheet with id=AD4, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.683A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.768A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.409A pdb=" N ILE H 35J" --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE H 50 " --> pdb=" O ILE H 35J" (cutoff:3.500A) removed outlier: 6.927A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 29 through 32 Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.570A pdb=" N ALA I 10 " --> pdb=" O ILE I 110 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE I 35J" --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE I 50 " --> pdb=" O ILE I 35J" (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.570A pdb=" N ALA I 10 " --> pdb=" O ILE I 110 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER I 102 " --> pdb=" O TRP I 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AE3, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.542A pdb=" N ALA I 35B" --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.388A pdb=" N ILE J 35J" --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE J 50 " --> pdb=" O ILE J 35J" (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 29 through 31 Processing sheet with id=AE7, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.708A pdb=" N VAL K 89 " --> pdb=" O SER K 39 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.959A pdb=" N SER K 96 " --> pdb=" O LEU K 100X" (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU K 100X" --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N HIS K 98 " --> pdb=" O SER K 100V" (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER K 100V" --> pdb=" O HIS K 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 100D through 100F removed outlier: 6.911A pdb=" N LEU K 100E" --> pdb=" O ASN K 100M" (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.931A pdb=" N VAL L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU L 73 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.621A pdb=" N ASP L 106 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS L 37 " --> pdb=" O ASN L 46 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN L 46 " --> pdb=" O HIS L 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.621A pdb=" N ASP L 106 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.611A pdb=" N ASP M 106 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE M 48 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS M 37 " --> pdb=" O ASN M 46 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASN M 46 " --> pdb=" O HIS M 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.611A pdb=" N ASP M 106 " --> pdb=" O LEU M 11 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.556A pdb=" N ASP N 106 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.556A pdb=" N ASP N 106 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL N 90 " --> pdb=" O SER N 97 " (cutoff:3.500A) 801 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6922 1.34 - 1.46: 5735 1.46 - 1.58: 9671 1.58 - 1.71: 1 1.71 - 1.83: 158 Bond restraints: 22487 Sorted by residual: bond pdb=" O2 TYS K 100F" pdb=" S TYS K 100F" ideal model delta sigma weight residual 1.461 1.633 -0.172 2.00e-02 2.50e+03 7.43e+01 bond pdb=" OH TYS K 100F" pdb=" S TYS K 100F" ideal model delta sigma weight residual 1.679 1.540 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C3 BMA j 3 " pdb=" O3 BMA j 3 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.12e+00 bond pdb=" C1 MAN m 5 " pdb=" C2 MAN m 5 " ideal model delta sigma weight residual 1.526 1.563 -0.037 2.00e-02 2.50e+03 3.42e+00 ... (remaining 22482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.67: 30522 5.67 - 11.34: 49 11.34 - 17.01: 2 17.01 - 22.69: 2 22.69 - 28.36: 2 Bond angle restraints: 30577 Sorted by residual: angle pdb=" O1 TYS K 100F" pdb=" S TYS K 100F" pdb=" O2 TYS K 100F" ideal model delta sigma weight residual 114.11 85.75 28.36 3.00e+00 1.11e-01 8.93e+01 angle pdb=" O2 TYS K 100F" pdb=" S TYS K 100F" pdb=" O3 TYS K 100F" ideal model delta sigma weight residual 115.38 87.47 27.91 3.00e+00 1.11e-01 8.66e+01 angle pdb=" OH TYS K 100F" pdb=" S TYS K 100F" pdb=" O2 TYS K 100F" ideal model delta sigma weight residual 104.74 85.21 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" OH TYS K 100F" pdb=" S TYS K 100F" pdb=" O3 TYS K 100F" ideal model delta sigma weight residual 100.21 119.65 -19.44 3.00e+00 1.11e-01 4.20e+01 angle pdb=" OH TYS K 100F" pdb=" S TYS K 100F" pdb=" O1 TYS K 100F" ideal model delta sigma weight residual 104.92 120.39 -15.47 3.00e+00 1.11e-01 2.66e+01 ... (remaining 30572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 12950 22.45 - 44.91: 1361 44.91 - 67.36: 250 67.36 - 89.82: 96 89.82 - 112.27: 45 Dihedral angle restraints: 14702 sinusoidal: 7077 harmonic: 7625 Sorted by residual: dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual 93.00 173.57 -80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS E 218 " pdb=" SG CYS E 218 " pdb=" SG CYS E 247 " pdb=" CB CYS E 247 " ideal model delta sinusoidal sigma weight residual 93.00 16.67 76.33 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.84 64.84 1 1.00e+01 1.00e-02 5.52e+01 ... (remaining 14699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3693 0.139 - 0.278: 38 0.278 - 0.417: 3 0.417 - 0.556: 0 0.556 - 0.695: 2 Chirality restraints: 3736 Sorted by residual: chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 363 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C 276 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN E 156 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 3733 not shown) Planarity restraints: 3793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 35 " 0.023 2.00e-02 2.50e+03 2.54e-02 1.61e+01 pdb=" CG TRP M 35 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP M 35 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP M 35 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 35 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 35 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 35 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 35 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP M 35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU L 79 " 0.058 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO L 80 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 79 " 0.050 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO M 80 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " 0.041 5.00e-02 4.00e+02 ... (remaining 3790 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 478 2.64 - 3.20: 20642 3.20 - 3.77: 34160 3.77 - 4.33: 43824 4.33 - 4.90: 73337 Nonbonded interactions: 172441 Sorted by model distance: nonbonded pdb=" OG SER A 334 " pdb=" OG1 THR A 337 " model vdw 2.075 3.040 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.106 3.040 nonbonded pdb=" O ILE A 277 " pdb=" NH2 ARG A 456 " model vdw 2.118 3.120 nonbonded pdb=" OG SER E 481 " pdb=" OE2 GLU E 482 " model vdw 2.126 3.040 nonbonded pdb=" OG SER I 74 " pdb=" O7 NAG n 1 " model vdw 2.148 3.040 ... (remaining 172436 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' and (resid 33 through 168 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB )) or resid 170 through 504 or resid 601 through 602)) selection = (chain 'C' and (resid 33 through 168 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB )) or resid 170 through 504 or resid 601 through 602)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain 'P' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' } ncs_group { reference = chain 'Q' selection = chain 'T' selection = chain 'j' } ncs_group { reference = (chain 'b' and (resid 2 or resid 5 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 6)) } 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: 11.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 50.970 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.006 0.172 22630 Z= 0.272 Angle : 0.871 28.357 30965 Z= 0.383 Chirality : 0.052 0.695 3736 Planarity : 0.004 0.089 3751 Dihedral : 19.202 112.274 9663 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.41 % Favored : 93.51 % Rotamer: Outliers : 0.57 % Allowed : 35.06 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2588 helix: 1.57 (0.29), residues: 375 sheet: 0.21 (0.19), residues: 761 loop : -0.75 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP M 35 HIS 0.008 0.001 HIS H 35K PHE 0.025 0.001 PHE G 98 TYR 0.025 0.002 TYR H 59 ARG 0.013 0.001 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 42) link_NAG-ASN : angle 2.51083 ( 126) link_ALPHA1-6 : bond 0.00247 ( 6) link_ALPHA1-6 : angle 2.00977 ( 18) link_BETA1-4 : bond 0.00646 ( 46) link_BETA1-4 : angle 2.48660 ( 138) link_ALPHA1-2 : bond 0.00187 ( 1) link_ALPHA1-2 : angle 2.25487 ( 3) link_ALPHA1-3 : bond 0.00414 ( 7) link_ALPHA1-3 : angle 2.31338 ( 21) hydrogen bonds : bond 0.12722 ( 773) hydrogen bonds : angle 6.40412 ( 2013) SS BOND : bond 0.00358 ( 41) SS BOND : angle 0.87092 ( 82) covalent geometry : bond 0.00594 (22487) covalent geometry : angle 0.83970 (30577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 399 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8004 (mmt) cc_final: 0.7674 (mmp) REVERT: B 584 GLU cc_start: 0.8626 (tt0) cc_final: 0.8199 (tm-30) outliers start: 13 outliers final: 10 residues processed: 407 average time/residue: 0.2936 time to fit residues: 191.3322 Evaluate side-chains 402 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 392 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain I residue 101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN E 137 ASN I 52 ASN I 64 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.060445 restraints weight = 65285.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.062445 restraints weight = 31765.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.063787 restraints weight = 19575.567| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22630 Z= 0.195 Angle : 0.700 9.804 30965 Z= 0.330 Chirality : 0.046 0.412 3736 Planarity : 0.004 0.046 3751 Dihedral : 12.364 87.011 4955 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 4.33 % Allowed : 30.37 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2588 helix: 2.05 (0.29), residues: 372 sheet: 0.17 (0.20), residues: 733 loop : -0.75 (0.17), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 35 HIS 0.004 0.001 HIS H 35K PHE 0.019 0.001 PHE N 91 TYR 0.023 0.002 TYR F 586 ARG 0.006 0.000 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 42) link_NAG-ASN : angle 2.24430 ( 126) link_ALPHA1-6 : bond 0.00353 ( 6) link_ALPHA1-6 : angle 2.14354 ( 18) link_BETA1-4 : bond 0.00595 ( 46) link_BETA1-4 : angle 2.42666 ( 138) link_ALPHA1-2 : bond 0.00595 ( 1) link_ALPHA1-2 : angle 2.60664 ( 3) link_ALPHA1-3 : bond 0.00658 ( 7) link_ALPHA1-3 : angle 2.52115 ( 21) hydrogen bonds : bond 0.03875 ( 773) hydrogen bonds : angle 5.50311 ( 2013) SS BOND : bond 0.00319 ( 41) SS BOND : angle 0.82380 ( 82) covalent geometry : bond 0.00444 (22487) covalent geometry : angle 0.66329 (30577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 414 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 543 ASN cc_start: 0.8571 (t0) cc_final: 0.7904 (t0) REVERT: B 588 ARG cc_start: 0.8369 (tpp-160) cc_final: 0.8036 (tmm-80) REVERT: B 595 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8992 (tp) REVERT: B 657 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8934 (tm-30) REVERT: C 180 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 423 ILE cc_start: 0.9485 (mp) cc_final: 0.9037 (mp) REVERT: F 586 TYR cc_start: 0.9445 (t80) cc_final: 0.9232 (t80) REVERT: I 46 GLU cc_start: 0.7815 (tt0) cc_final: 0.7606 (tt0) REVERT: I 54 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8971 (mmt180) REVERT: I 83 LYS cc_start: 0.9230 (mmmm) cc_final: 0.9010 (mmmm) REVERT: J 31 TYR cc_start: 0.8608 (t80) cc_final: 0.8393 (t80) REVERT: L 27 GLN cc_start: 0.8319 (tp40) cc_final: 0.7947 (tm-30) REVERT: L 28 ASP cc_start: 0.8554 (t0) cc_final: 0.8317 (t0) REVERT: L 73 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7309 (tt) outliers start: 98 outliers final: 50 residues processed: 479 average time/residue: 0.3002 time to fit residues: 233.7242 Evaluate side-chains 442 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 388 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 2 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 205 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN C 130 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN I 64 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.071591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.059948 restraints weight = 65191.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061951 restraints weight = 31893.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.063321 restraints weight = 19737.350| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22630 Z= 0.202 Angle : 0.684 10.189 30965 Z= 0.322 Chirality : 0.047 0.391 3736 Planarity : 0.003 0.034 3751 Dihedral : 10.733 79.232 4943 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 5.84 % Allowed : 29.13 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2588 helix: 2.10 (0.28), residues: 375 sheet: 0.28 (0.20), residues: 697 loop : -0.84 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 35 HIS 0.004 0.001 HIS N 37 PHE 0.017 0.001 PHE N 91 TYR 0.018 0.002 TYR E 217 ARG 0.005 0.000 ARG N 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 42) link_NAG-ASN : angle 2.26169 ( 126) link_ALPHA1-6 : bond 0.00419 ( 6) link_ALPHA1-6 : angle 2.02283 ( 18) link_BETA1-4 : bond 0.00597 ( 46) link_BETA1-4 : angle 2.37860 ( 138) link_ALPHA1-2 : bond 0.00509 ( 1) link_ALPHA1-2 : angle 2.59059 ( 3) link_ALPHA1-3 : bond 0.00760 ( 7) link_ALPHA1-3 : angle 2.36896 ( 21) hydrogen bonds : bond 0.03778 ( 773) hydrogen bonds : angle 5.30595 ( 2013) SS BOND : bond 0.00332 ( 41) SS BOND : angle 0.80043 ( 82) covalent geometry : bond 0.00459 (22487) covalent geometry : angle 0.64725 (30577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 406 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8971 (t0) cc_final: 0.8768 (t0) REVERT: A 378 CYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7005 (t) REVERT: B 543 ASN cc_start: 0.8585 (t0) cc_final: 0.7951 (t0) REVERT: B 588 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.7977 (tmm-80) REVERT: B 595 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 657 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8900 (tm-30) REVERT: C 180 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.7663 (t0) REVERT: C 423 ILE cc_start: 0.9626 (mp) cc_final: 0.9126 (mp) REVERT: G 45 GLN cc_start: 0.8244 (mm-40) cc_final: 0.8032 (mm110) REVERT: G 77 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8142 (ttp-110) REVERT: I 38 ARG cc_start: 0.8770 (ptt180) cc_final: 0.8484 (ptt180) REVERT: I 54 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.9033 (mmt180) REVERT: I 71 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8640 (pmt170) REVERT: I 83 LYS cc_start: 0.9234 (mmmm) cc_final: 0.9011 (mmmm) REVERT: L 27 GLN cc_start: 0.8306 (tp40) cc_final: 0.7873 (tm-30) REVERT: L 28 ASP cc_start: 0.8529 (t0) cc_final: 0.8256 (t0) REVERT: M 70 TYR cc_start: 0.8189 (t80) cc_final: 0.7967 (t80) outliers start: 132 outliers final: 78 residues processed: 501 average time/residue: 0.4358 time to fit residues: 355.1813 Evaluate side-chains 468 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 385 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 97 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 8 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 0.0060 chunk 221 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 218 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN H 39 GLN I 64 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061971 restraints weight = 64981.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.064030 restraints weight = 31568.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.065412 restraints weight = 19366.081| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22630 Z= 0.121 Angle : 0.648 9.856 30965 Z= 0.303 Chirality : 0.046 0.415 3736 Planarity : 0.003 0.034 3751 Dihedral : 9.469 68.751 4943 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 4.86 % Allowed : 30.19 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2588 helix: 2.25 (0.28), residues: 372 sheet: 0.30 (0.20), residues: 757 loop : -0.73 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 479 HIS 0.004 0.001 HIS N 37 PHE 0.015 0.001 PHE N 91 TYR 0.023 0.001 TYR F 586 ARG 0.005 0.000 ARG N 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 42) link_NAG-ASN : angle 2.03636 ( 126) link_ALPHA1-6 : bond 0.00523 ( 6) link_ALPHA1-6 : angle 1.93279 ( 18) link_BETA1-4 : bond 0.00592 ( 46) link_BETA1-4 : angle 2.23028 ( 138) link_ALPHA1-2 : bond 0.00794 ( 1) link_ALPHA1-2 : angle 2.18358 ( 3) link_ALPHA1-3 : bond 0.00842 ( 7) link_ALPHA1-3 : angle 2.40953 ( 21) hydrogen bonds : bond 0.03346 ( 773) hydrogen bonds : angle 5.10844 ( 2013) SS BOND : bond 0.00351 ( 41) SS BOND : angle 0.72161 ( 82) covalent geometry : bond 0.00276 (22487) covalent geometry : angle 0.61452 (30577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 449 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: B 543 ASN cc_start: 0.8556 (t0) cc_final: 0.7986 (t0) REVERT: B 588 ARG cc_start: 0.8336 (tpp-160) cc_final: 0.8013 (tmm-80) REVERT: B 595 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8933 (tp) REVERT: B 657 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8836 (tm-30) REVERT: C 178 ARG cc_start: 0.8337 (tpt170) cc_final: 0.7931 (tpt170) REVERT: C 180 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.7535 (t0) REVERT: C 304 ARG cc_start: 0.9560 (OUTLIER) cc_final: 0.9336 (ptm-80) REVERT: C 423 ILE cc_start: 0.9633 (mp) cc_final: 0.9212 (mp) REVERT: C 486 TYR cc_start: 0.9431 (m-80) cc_final: 0.9199 (m-80) REVERT: D 530 MET cc_start: 0.8316 (mpp) cc_final: 0.7759 (mpp) REVERT: E 177 TYR cc_start: 0.8952 (m-80) cc_final: 0.8685 (m-10) REVERT: G 45 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7955 (mm110) REVERT: G 89 MET cc_start: 0.8644 (mmm) cc_final: 0.8358 (mmm) REVERT: I 38 ARG cc_start: 0.8679 (ptt180) cc_final: 0.8442 (ptt180) REVERT: I 46 GLU cc_start: 0.7792 (tt0) cc_final: 0.7406 (tt0) REVERT: I 54 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.9003 (mmt180) REVERT: I 71 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8632 (pmt170) REVERT: I 83 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8993 (mmmm) REVERT: I 86 ASP cc_start: 0.8741 (m-30) cc_final: 0.8483 (m-30) REVERT: J 46 GLU cc_start: 0.7963 (tp30) cc_final: 0.7720 (tp30) REVERT: L 27 GLN cc_start: 0.8227 (tp40) cc_final: 0.7810 (tm-30) REVERT: L 28 ASP cc_start: 0.8438 (t0) cc_final: 0.8178 (t0) REVERT: M 35 TRP cc_start: 0.8957 (m100) cc_final: 0.8566 (m100) outliers start: 110 outliers final: 68 residues processed: 531 average time/residue: 0.3195 time to fit residues: 272.8314 Evaluate side-chains 487 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 413 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 97 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 226 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 130 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN D 658 GLN I 64 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062055 restraints weight = 64721.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064094 restraints weight = 31871.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065443 restraints weight = 19702.724| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22630 Z= 0.133 Angle : 0.652 10.030 30965 Z= 0.303 Chirality : 0.046 0.411 3736 Planarity : 0.003 0.033 3751 Dihedral : 8.829 64.351 4941 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 5.13 % Allowed : 30.99 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2588 helix: 2.17 (0.28), residues: 375 sheet: 0.27 (0.19), residues: 775 loop : -0.72 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 596 HIS 0.005 0.001 HIS N 37 PHE 0.013 0.001 PHE M 62 TYR 0.018 0.001 TYR F 586 ARG 0.006 0.000 ARG M 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 42) link_NAG-ASN : angle 2.05392 ( 126) link_ALPHA1-6 : bond 0.00549 ( 6) link_ALPHA1-6 : angle 1.90147 ( 18) link_BETA1-4 : bond 0.00585 ( 46) link_BETA1-4 : angle 2.17820 ( 138) link_ALPHA1-2 : bond 0.00772 ( 1) link_ALPHA1-2 : angle 2.17462 ( 3) link_ALPHA1-3 : bond 0.00875 ( 7) link_ALPHA1-3 : angle 2.43372 ( 21) hydrogen bonds : bond 0.03288 ( 773) hydrogen bonds : angle 5.02414 ( 2013) SS BOND : bond 0.00271 ( 41) SS BOND : angle 0.69964 ( 82) covalent geometry : bond 0.00309 (22487) covalent geometry : angle 0.61902 (30577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 433 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: B 543 ASN cc_start: 0.8516 (t0) cc_final: 0.7990 (t0) REVERT: B 588 ARG cc_start: 0.8352 (tpp-160) cc_final: 0.8049 (tmm-80) REVERT: B 595 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8936 (tp) REVERT: B 657 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 178 ARG cc_start: 0.8344 (tpt170) cc_final: 0.7965 (tpt170) REVERT: C 180 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.7549 (t0) REVERT: C 423 ILE cc_start: 0.9653 (mp) cc_final: 0.9239 (mp) REVERT: C 486 TYR cc_start: 0.9398 (m-80) cc_final: 0.9155 (m-80) REVERT: D 530 MET cc_start: 0.8332 (mpp) cc_final: 0.7771 (mpp) REVERT: D 601 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8629 (mmmm) REVERT: E 375 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8765 (p) REVERT: F 577 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7909 (tp40) REVERT: I 38 ARG cc_start: 0.8616 (ptt180) cc_final: 0.8410 (ptt180) REVERT: I 54 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8978 (mmt180) REVERT: I 62 ARG cc_start: 0.8772 (ttp-110) cc_final: 0.8569 (ptp-110) REVERT: I 71 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8577 (pmt170) REVERT: I 86 ASP cc_start: 0.8757 (m-30) cc_final: 0.8506 (m-30) REVERT: J 46 GLU cc_start: 0.7937 (tp30) cc_final: 0.7698 (tp30) REVERT: L 27 GLN cc_start: 0.8254 (tp40) cc_final: 0.7836 (tm-30) REVERT: L 28 ASP cc_start: 0.8389 (t0) cc_final: 0.8146 (t0) REVERT: M 35 TRP cc_start: 0.8955 (m100) cc_final: 0.8527 (m100) outliers start: 116 outliers final: 81 residues processed: 519 average time/residue: 0.4387 time to fit residues: 372.5349 Evaluate side-chains 498 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 410 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 97 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 45 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 79 optimal weight: 0.0030 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.3064 r_free = 0.3064 target = 0.072253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.060531 restraints weight = 65229.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.062542 restraints weight = 32024.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.063891 restraints weight = 19872.403| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22630 Z= 0.188 Angle : 0.671 9.956 30965 Z= 0.314 Chirality : 0.046 0.398 3736 Planarity : 0.003 0.049 3751 Dihedral : 8.526 66.980 4940 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 5.57 % Allowed : 30.46 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2588 helix: 2.20 (0.28), residues: 375 sheet: 0.22 (0.20), residues: 754 loop : -0.78 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 596 HIS 0.005 0.001 HIS N 37 PHE 0.016 0.001 PHE M 62 TYR 0.022 0.002 TYR E 217 ARG 0.007 0.000 ARG N 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 42) link_NAG-ASN : angle 2.16846 ( 126) link_ALPHA1-6 : bond 0.00554 ( 6) link_ALPHA1-6 : angle 1.92154 ( 18) link_BETA1-4 : bond 0.00550 ( 46) link_BETA1-4 : angle 2.19238 ( 138) link_ALPHA1-2 : bond 0.00604 ( 1) link_ALPHA1-2 : angle 2.34533 ( 3) link_ALPHA1-3 : bond 0.00811 ( 7) link_ALPHA1-3 : angle 2.54482 ( 21) hydrogen bonds : bond 0.03375 ( 773) hydrogen bonds : angle 5.00901 ( 2013) SS BOND : bond 0.00311 ( 41) SS BOND : angle 0.78275 ( 82) covalent geometry : bond 0.00429 (22487) covalent geometry : angle 0.63761 (30577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 410 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 CYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6948 (t) REVERT: B 543 ASN cc_start: 0.8627 (t0) cc_final: 0.8056 (t0) REVERT: B 588 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8012 (tmm-80) REVERT: B 595 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8964 (tp) REVERT: B 657 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8848 (tm-30) REVERT: C 104 MET cc_start: 0.8882 (ttp) cc_final: 0.8594 (ttp) REVERT: C 178 ARG cc_start: 0.8412 (tpt170) cc_final: 0.8058 (tpt170) REVERT: C 180 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.7669 (t0) REVERT: C 423 ILE cc_start: 0.9676 (mp) cc_final: 0.9256 (mp) REVERT: C 486 TYR cc_start: 0.9448 (m-80) cc_final: 0.9142 (m-80) REVERT: D 530 MET cc_start: 0.8409 (mpp) cc_final: 0.7773 (mpp) REVERT: D 601 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8800 (mmmm) REVERT: F 586 TYR cc_start: 0.9451 (t80) cc_final: 0.9195 (t80) REVERT: I 35 TYR cc_start: 0.9105 (m-80) cc_final: 0.8900 (m-80) REVERT: I 54 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8858 (mmt180) REVERT: I 71 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8614 (pmt170) REVERT: I 86 ASP cc_start: 0.8798 (m-30) cc_final: 0.8561 (m-30) REVERT: J 46 GLU cc_start: 0.8023 (tp30) cc_final: 0.7757 (tp30) REVERT: L 27 GLN cc_start: 0.8306 (tp40) cc_final: 0.7830 (tm-30) REVERT: L 28 ASP cc_start: 0.8467 (t0) cc_final: 0.8195 (t0) REVERT: M 35 TRP cc_start: 0.9108 (m100) cc_final: 0.8583 (m100) outliers start: 126 outliers final: 97 residues processed: 504 average time/residue: 0.2999 time to fit residues: 242.2769 Evaluate side-chains 504 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 402 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 127 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN C 130 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 651 ASN I 64 GLN L 37 HIS ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.074279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.062654 restraints weight = 64479.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.064678 restraints weight = 31796.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.066026 restraints weight = 19688.912| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22630 Z= 0.117 Angle : 0.649 10.870 30965 Z= 0.305 Chirality : 0.045 0.416 3736 Planarity : 0.003 0.037 3751 Dihedral : 8.089 68.237 4940 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 4.55 % Allowed : 31.96 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2588 helix: 2.23 (0.28), residues: 375 sheet: 0.28 (0.20), residues: 778 loop : -0.72 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 427 HIS 0.004 0.001 HIS N 37 PHE 0.013 0.001 PHE N 91 TYR 0.018 0.001 TYR E 217 ARG 0.005 0.000 ARG M 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 42) link_NAG-ASN : angle 2.00076 ( 126) link_ALPHA1-6 : bond 0.00577 ( 6) link_ALPHA1-6 : angle 1.70952 ( 18) link_BETA1-4 : bond 0.00594 ( 46) link_BETA1-4 : angle 2.05584 ( 138) link_ALPHA1-2 : bond 0.00884 ( 1) link_ALPHA1-2 : angle 2.03884 ( 3) link_ALPHA1-3 : bond 0.00882 ( 7) link_ALPHA1-3 : angle 2.38815 ( 21) hydrogen bonds : bond 0.03164 ( 773) hydrogen bonds : angle 4.92700 ( 2013) SS BOND : bond 0.00258 ( 41) SS BOND : angle 0.72651 ( 82) covalent geometry : bond 0.00267 (22487) covalent geometry : angle 0.61967 (30577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 441 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: B 543 ASN cc_start: 0.8516 (t0) cc_final: 0.7955 (t0) REVERT: B 588 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.8051 (tmm-80) REVERT: B 595 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8933 (tp) REVERT: B 657 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 104 MET cc_start: 0.8778 (ttp) cc_final: 0.8450 (ttp) REVERT: C 178 ARG cc_start: 0.8334 (tpt170) cc_final: 0.8039 (tpt170) REVERT: C 180 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.7566 (t0) REVERT: C 423 ILE cc_start: 0.9670 (mp) cc_final: 0.9254 (mp) REVERT: C 486 TYR cc_start: 0.9359 (m-80) cc_final: 0.9113 (m-80) REVERT: D 530 MET cc_start: 0.8316 (mpp) cc_final: 0.7686 (mpp) REVERT: D 601 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8625 (mmmm) REVERT: D 624 ASP cc_start: 0.8028 (m-30) cc_final: 0.7795 (m-30) REVERT: E 375 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8714 (p) REVERT: F 586 TYR cc_start: 0.9429 (t80) cc_final: 0.8864 (t80) REVERT: I 46 GLU cc_start: 0.7822 (tt0) cc_final: 0.7491 (tt0) REVERT: I 54 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.9014 (mmt180) REVERT: I 71 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8577 (pmt170) REVERT: I 83 LYS cc_start: 0.9104 (mmtp) cc_final: 0.8898 (mmmm) REVERT: I 86 ASP cc_start: 0.8727 (m-30) cc_final: 0.8505 (m-30) REVERT: J 43 GLN cc_start: 0.8435 (mp10) cc_final: 0.7935 (mp10) REVERT: J 46 GLU cc_start: 0.7909 (tp30) cc_final: 0.7693 (tp30) REVERT: L 27 GLN cc_start: 0.8252 (tp40) cc_final: 0.7875 (tm-30) REVERT: L 28 ASP cc_start: 0.8377 (t0) cc_final: 0.8115 (t0) REVERT: M 35 TRP cc_start: 0.8969 (m100) cc_final: 0.8498 (m100) REVERT: N 61 ARG cc_start: 0.8558 (mtp180) cc_final: 0.8239 (mtm110) outliers start: 103 outliers final: 81 residues processed: 513 average time/residue: 0.3185 time to fit residues: 263.3446 Evaluate side-chains 496 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 409 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 167 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 128 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.3096 r_free = 0.3096 target = 0.073841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062047 restraints weight = 64930.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064101 restraints weight = 31878.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065479 restraints weight = 19693.092| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22630 Z= 0.134 Angle : 0.657 11.652 30965 Z= 0.307 Chirality : 0.045 0.410 3736 Planarity : 0.003 0.034 3751 Dihedral : 7.849 68.221 4940 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 4.60 % Allowed : 32.18 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2588 helix: 2.22 (0.28), residues: 375 sheet: 0.32 (0.20), residues: 748 loop : -0.71 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 35 HIS 0.004 0.001 HIS N 37 PHE 0.012 0.001 PHE N 91 TYR 0.019 0.001 TYR F 586 ARG 0.007 0.000 ARG M 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 42) link_NAG-ASN : angle 2.02912 ( 126) link_ALPHA1-6 : bond 0.00565 ( 6) link_ALPHA1-6 : angle 1.70005 ( 18) link_BETA1-4 : bond 0.00576 ( 46) link_BETA1-4 : angle 2.03532 ( 138) link_ALPHA1-2 : bond 0.00822 ( 1) link_ALPHA1-2 : angle 2.07095 ( 3) link_ALPHA1-3 : bond 0.00844 ( 7) link_ALPHA1-3 : angle 2.36216 ( 21) hydrogen bonds : bond 0.03172 ( 773) hydrogen bonds : angle 4.88239 ( 2013) SS BOND : bond 0.00273 ( 41) SS BOND : angle 0.71420 ( 82) covalent geometry : bond 0.00308 (22487) covalent geometry : angle 0.62736 (30577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 428 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: A 378 CYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6950 (t) REVERT: B 543 ASN cc_start: 0.8547 (t0) cc_final: 0.7975 (t0) REVERT: B 588 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.8029 (tmm-80) REVERT: B 595 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8937 (tp) REVERT: B 657 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8825 (tm-30) REVERT: C 150 MET cc_start: 0.9076 (mmp) cc_final: 0.8685 (mmt) REVERT: C 178 ARG cc_start: 0.8374 (tpt170) cc_final: 0.7982 (tpt170) REVERT: C 180 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.7587 (t0) REVERT: C 423 ILE cc_start: 0.9677 (mp) cc_final: 0.9256 (mp) REVERT: C 486 TYR cc_start: 0.9375 (m-80) cc_final: 0.9131 (m-80) REVERT: D 530 MET cc_start: 0.8317 (mpp) cc_final: 0.7687 (mpp) REVERT: D 601 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8686 (mmmm) REVERT: D 624 ASP cc_start: 0.8075 (m-30) cc_final: 0.7823 (m-30) REVERT: E 153 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7554 (tp30) REVERT: E 375 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8664 (p) REVERT: I 54 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.9038 (mmt180) REVERT: I 71 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8546 (pmt170) REVERT: I 83 LYS cc_start: 0.9140 (mmtp) cc_final: 0.8925 (mmmm) REVERT: I 86 ASP cc_start: 0.8766 (m-30) cc_final: 0.8527 (m-30) REVERT: J 35 GLU cc_start: 0.7562 (tp30) cc_final: 0.7197 (tp30) REVERT: J 43 GLN cc_start: 0.8413 (mp10) cc_final: 0.7919 (mp10) REVERT: J 46 GLU cc_start: 0.7955 (tp30) cc_final: 0.7723 (tp30) REVERT: L 27 GLN cc_start: 0.8300 (tp40) cc_final: 0.7901 (tm-30) REVERT: L 28 ASP cc_start: 0.8417 (t0) cc_final: 0.8170 (t0) REVERT: M 35 TRP cc_start: 0.9008 (m100) cc_final: 0.8491 (m100) REVERT: N 61 ARG cc_start: 0.8555 (mtp180) cc_final: 0.8121 (mtm110) outliers start: 104 outliers final: 84 residues processed: 504 average time/residue: 0.3185 time to fit residues: 254.6493 Evaluate side-chains 508 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 417 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 97 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 79 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 150 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.074743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.063030 restraints weight = 64676.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.065081 restraints weight = 31637.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.066439 restraints weight = 19550.305| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22630 Z= 0.119 Angle : 0.663 13.320 30965 Z= 0.310 Chirality : 0.046 0.413 3736 Planarity : 0.003 0.036 3751 Dihedral : 7.656 67.923 4940 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 4.47 % Allowed : 32.40 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2588 helix: 2.10 (0.28), residues: 381 sheet: 0.31 (0.20), residues: 774 loop : -0.72 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS N 37 PHE 0.017 0.001 PHE C 159 TYR 0.019 0.001 TYR K 100C ARG 0.006 0.000 ARG M 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 42) link_NAG-ASN : angle 1.94866 ( 126) link_ALPHA1-6 : bond 0.00589 ( 6) link_ALPHA1-6 : angle 1.61716 ( 18) link_BETA1-4 : bond 0.00590 ( 46) link_BETA1-4 : angle 1.96736 ( 138) link_ALPHA1-2 : bond 0.00932 ( 1) link_ALPHA1-2 : angle 1.93180 ( 3) link_ALPHA1-3 : bond 0.00844 ( 7) link_ALPHA1-3 : angle 2.27099 ( 21) hydrogen bonds : bond 0.03106 ( 773) hydrogen bonds : angle 4.84019 ( 2013) SS BOND : bond 0.00258 ( 41) SS BOND : angle 0.71401 ( 82) covalent geometry : bond 0.00277 (22487) covalent geometry : angle 0.63608 (30577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 444 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: A 378 CYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6897 (t) REVERT: B 543 ASN cc_start: 0.8555 (t0) cc_final: 0.8037 (t0) REVERT: B 588 ARG cc_start: 0.8327 (tpp-160) cc_final: 0.8021 (tmm-80) REVERT: B 595 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8910 (tp) REVERT: B 657 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8826 (tm-30) REVERT: C 150 MET cc_start: 0.9062 (mmp) cc_final: 0.8546 (mmt) REVERT: C 178 ARG cc_start: 0.8366 (tpt170) cc_final: 0.8062 (tpt170) REVERT: C 180 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.7575 (t0) REVERT: C 423 ILE cc_start: 0.9670 (mp) cc_final: 0.9313 (mp) REVERT: C 466 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: C 486 TYR cc_start: 0.9345 (m-80) cc_final: 0.9105 (m-80) REVERT: D 530 MET cc_start: 0.8313 (mpp) cc_final: 0.7692 (mpp) REVERT: D 601 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8639 (mmmm) REVERT: D 624 ASP cc_start: 0.8045 (m-30) cc_final: 0.7780 (m-30) REVERT: E 153 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7562 (tp30) REVERT: E 375 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8641 (p) REVERT: I 54 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.9030 (mmt180) REVERT: I 71 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8536 (pmt170) REVERT: I 83 LYS cc_start: 0.9156 (mmtp) cc_final: 0.8922 (mmmm) REVERT: I 86 ASP cc_start: 0.8768 (m-30) cc_final: 0.8457 (m-30) REVERT: J 35 GLU cc_start: 0.7606 (tp30) cc_final: 0.7399 (tp30) REVERT: J 43 GLN cc_start: 0.8410 (mp10) cc_final: 0.7885 (mp10) REVERT: K 100 TYR cc_start: 0.8585 (m-10) cc_final: 0.8272 (m-10) REVERT: L 27 GLN cc_start: 0.8314 (tp40) cc_final: 0.7885 (tm-30) REVERT: M 35 TRP cc_start: 0.8980 (m100) cc_final: 0.8464 (m100) REVERT: N 61 ARG cc_start: 0.8550 (mtp180) cc_final: 0.8329 (mtm110) outliers start: 101 outliers final: 81 residues processed: 516 average time/residue: 0.3381 time to fit residues: 278.6357 Evaluate side-chains 511 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 422 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 148 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN I 64 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.3076 r_free = 0.3076 target = 0.072857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.061048 restraints weight = 65572.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.063077 restraints weight = 32311.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064482 restraints weight = 20020.129| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22630 Z= 0.179 Angle : 0.690 14.264 30965 Z= 0.323 Chirality : 0.045 0.398 3736 Planarity : 0.003 0.039 3751 Dihedral : 7.653 66.962 4940 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 4.20 % Allowed : 32.94 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2588 helix: 2.09 (0.28), residues: 381 sheet: 0.14 (0.19), residues: 807 loop : -0.69 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 479 HIS 0.004 0.001 HIS N 37 PHE 0.017 0.001 PHE C 159 TYR 0.024 0.002 TYR F 586 ARG 0.006 0.000 ARG N 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 42) link_NAG-ASN : angle 2.10102 ( 126) link_ALPHA1-6 : bond 0.00539 ( 6) link_ALPHA1-6 : angle 1.69904 ( 18) link_BETA1-4 : bond 0.00539 ( 46) link_BETA1-4 : angle 2.03081 ( 138) link_ALPHA1-2 : bond 0.00716 ( 1) link_ALPHA1-2 : angle 2.14869 ( 3) link_ALPHA1-3 : bond 0.00791 ( 7) link_ALPHA1-3 : angle 2.35309 ( 21) hydrogen bonds : bond 0.03301 ( 773) hydrogen bonds : angle 4.85965 ( 2013) SS BOND : bond 0.00310 ( 41) SS BOND : angle 0.74250 ( 82) covalent geometry : bond 0.00411 (22487) covalent geometry : angle 0.66144 (30577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 408 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 CYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6982 (t) REVERT: B 543 ASN cc_start: 0.8580 (t0) cc_final: 0.8037 (t0) REVERT: B 588 ARG cc_start: 0.8346 (tpp-160) cc_final: 0.8012 (tmm-80) REVERT: B 595 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8947 (tp) REVERT: B 657 GLU cc_start: 0.9320 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 150 MET cc_start: 0.9115 (mmp) cc_final: 0.8643 (mmt) REVERT: C 178 ARG cc_start: 0.8405 (tpt170) cc_final: 0.8098 (tpt170) REVERT: C 180 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.7685 (t0) REVERT: C 423 ILE cc_start: 0.9677 (mp) cc_final: 0.9271 (mp) REVERT: C 466 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 486 TYR cc_start: 0.9407 (m-80) cc_final: 0.9149 (m-80) REVERT: D 530 MET cc_start: 0.8324 (mpp) cc_final: 0.7722 (mpp) REVERT: D 624 ASP cc_start: 0.8109 (m-30) cc_final: 0.7826 (m-30) REVERT: E 104 MET cc_start: 0.9111 (ttp) cc_final: 0.8731 (ttp) REVERT: E 375 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8784 (p) REVERT: I 54 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.9043 (mmt180) REVERT: I 71 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8612 (pmt170) REVERT: I 83 LYS cc_start: 0.9183 (mmtp) cc_final: 0.8927 (mmmm) REVERT: J 35 GLU cc_start: 0.7678 (tp30) cc_final: 0.7458 (tp30) REVERT: J 43 GLN cc_start: 0.8434 (mp10) cc_final: 0.7898 (mp10) REVERT: L 27 GLN cc_start: 0.8354 (tp40) cc_final: 0.7888 (tm-30) REVERT: L 28 ASP cc_start: 0.8465 (t0) cc_final: 0.8004 (t0) REVERT: M 35 TRP cc_start: 0.9069 (m100) cc_final: 0.8471 (m100) REVERT: N 61 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8387 (mtm110) outliers start: 95 outliers final: 82 residues processed: 475 average time/residue: 0.3053 time to fit residues: 233.9005 Evaluate side-chains 496 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 407 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 217 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.0040 chunk 132 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.3071 r_free = 0.3071 target = 0.072605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.060834 restraints weight = 65267.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.062848 restraints weight = 32094.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064224 restraints weight = 19906.559| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22630 Z= 0.182 Angle : 0.695 13.674 30965 Z= 0.326 Chirality : 0.046 0.397 3736 Planarity : 0.003 0.034 3751 Dihedral : 7.646 65.853 4940 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 4.29 % Allowed : 32.80 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2588 helix: 2.07 (0.28), residues: 381 sheet: 0.11 (0.19), residues: 807 loop : -0.72 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 479 HIS 0.004 0.001 HIS N 37 PHE 0.014 0.001 PHE N 91 TYR 0.021 0.002 TYR K 100C ARG 0.006 0.000 ARG M 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 42) link_NAG-ASN : angle 2.11927 ( 126) link_ALPHA1-6 : bond 0.00544 ( 6) link_ALPHA1-6 : angle 1.69612 ( 18) link_BETA1-4 : bond 0.00545 ( 46) link_BETA1-4 : angle 2.03179 ( 138) link_ALPHA1-2 : bond 0.00711 ( 1) link_ALPHA1-2 : angle 2.19126 ( 3) link_ALPHA1-3 : bond 0.00772 ( 7) link_ALPHA1-3 : angle 2.35023 ( 21) hydrogen bonds : bond 0.03311 ( 773) hydrogen bonds : angle 4.88435 ( 2013) SS BOND : bond 0.00314 ( 41) SS BOND : angle 0.75669 ( 82) covalent geometry : bond 0.00420 (22487) covalent geometry : angle 0.66626 (30577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8154.76 seconds wall clock time: 146 minutes 24.40 seconds (8784.40 seconds total)