Starting phenix.real_space_refine on Sun Aug 24 18:19:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ulu_42366/08_2025/8ulu_42366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ulu_42366/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ulu_42366/08_2025/8ulu_42366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ulu_42366/08_2025/8ulu_42366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ulu_42366/08_2025/8ulu_42366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ulu_42366/08_2025/8ulu_42366.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.79, per 1000 atoms: 0.26 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: 2.44 Conformation dependent library (CDL) restraints added in 929.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.06 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: 5.08 Time building geometry restraints manager: 3.04 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 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 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: 7.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.570 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- 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 : 15.10 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG F 617 TYR 0.025 0.002 TYR H 59 PHE 0.025 0.001 PHE G 98 TRP 0.066 0.002 TRP M 35 HIS 0.008 0.001 HIS H 35K Details of bonding type rmsd covalent geometry : bond 0.00594 (22487) covalent geometry : angle 0.83970 (30577) SS BOND : bond 0.00358 ( 41) SS BOND : angle 0.87092 ( 82) hydrogen bonds : bond 0.12722 ( 773) hydrogen bonds : angle 6.40412 ( 2013) 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) 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_NAG-ASN : bond 0.00360 ( 42) link_NAG-ASN : angle 2.51083 ( 126) *********************** 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 : 0.948 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: 0.1475 time to fit residues: 96.7361 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 : 0.864 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 136 ASN E 137 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.058804 restraints weight = 66266.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.060771 restraints weight = 32664.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062091 restraints weight = 20336.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.062983 restraints weight = 14746.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.063583 restraints weight = 11737.975| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 22630 Z= 0.299 Angle : 0.770 10.587 30965 Z= 0.363 Chirality : 0.048 0.415 3736 Planarity : 0.004 0.045 3751 Dihedral : 12.257 88.728 4955 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 5.48 % Allowed : 29.75 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2588 helix: 1.86 (0.28), residues: 372 sheet: 0.20 (0.20), residues: 687 loop : -0.91 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 617 TYR 0.025 0.002 TYR F 586 PHE 0.020 0.002 PHE N 91 TRP 0.029 0.002 TRP M 35 HIS 0.005 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00679 (22487) covalent geometry : angle 0.72983 (30577) SS BOND : bond 0.00409 ( 41) SS BOND : angle 0.92661 ( 82) hydrogen bonds : bond 0.04216 ( 773) hydrogen bonds : angle 5.61374 ( 2013) link_ALPHA1-2 : bond 0.00297 ( 1) link_ALPHA1-2 : angle 3.02157 ( 3) link_ALPHA1-3 : bond 0.00746 ( 7) link_ALPHA1-3 : angle 2.75499 ( 21) link_ALPHA1-6 : bond 0.00414 ( 6) link_ALPHA1-6 : angle 2.42313 ( 18) link_BETA1-4 : bond 0.00667 ( 46) link_BETA1-4 : angle 2.59168 ( 138) link_NAG-ASN : bond 0.00577 ( 42) link_NAG-ASN : angle 2.51309 ( 126) *********************** 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 507 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 383 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 CYS cc_start: 0.7262 (OUTLIER) cc_final: 0.7003 (t) REVERT: B 530 MET cc_start: 0.8225 (mmt) cc_final: 0.7737 (mmm) REVERT: B 543 ASN cc_start: 0.8501 (t0) cc_final: 0.7843 (t0) REVERT: B 588 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8145 (tmm-80) REVERT: B 595 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9067 (tp) REVERT: B 657 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8928 (tm-30) REVERT: C 180 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.7940 (t0) REVERT: C 423 ILE cc_start: 0.9615 (mp) cc_final: 0.9032 (mp) REVERT: H 72 ASP cc_start: 0.8685 (t0) cc_final: 0.8411 (t0) REVERT: I 54 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.9010 (mmt180) REVERT: I 71 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8690 (pmt170) REVERT: I 83 LYS cc_start: 0.9235 (mmmm) cc_final: 0.9021 (mmmm) REVERT: L 27 GLN cc_start: 0.8375 (tp40) cc_final: 0.8014 (tm-30) outliers start: 124 outliers final: 67 residues processed: 474 average time/residue: 0.1451 time to fit residues: 111.3661 Evaluate side-chains 436 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 364 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 271 MET 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 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 106 THR 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 278 THR Chi-restraints excluded: chain C residue 345 VAL 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 593 LEU 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 68 VAL 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 345 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 660 LEU 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 I residue 71 ARG 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 J residue 67 ILE Chi-restraints excluded: chain J residue 68 THR 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 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 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 212 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.060784 restraints weight = 65078.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062779 restraints weight = 31997.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.064148 restraints weight = 19797.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.065017 restraints weight = 14136.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065649 restraints weight = 11225.750| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22630 Z= 0.151 Angle : 0.670 9.736 30965 Z= 0.315 Chirality : 0.046 0.400 3736 Planarity : 0.003 0.033 3751 Dihedral : 10.817 78.527 4943 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 4.60 % Allowed : 30.73 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2588 helix: 2.14 (0.28), residues: 372 sheet: 0.21 (0.20), residues: 703 loop : -0.85 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 42 TYR 0.023 0.001 TYR F 586 PHE 0.018 0.001 PHE N 91 TRP 0.026 0.001 TRP C 69 HIS 0.004 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00345 (22487) covalent geometry : angle 0.63397 (30577) SS BOND : bond 0.00311 ( 41) SS BOND : angle 0.78166 ( 82) hydrogen bonds : bond 0.03673 ( 773) hydrogen bonds : angle 5.29875 ( 2013) link_ALPHA1-2 : bond 0.00678 ( 1) link_ALPHA1-2 : angle 2.42562 ( 3) link_ALPHA1-3 : bond 0.00781 ( 7) link_ALPHA1-3 : angle 2.30892 ( 21) link_ALPHA1-6 : bond 0.00419 ( 6) link_ALPHA1-6 : angle 1.98230 ( 18) link_BETA1-4 : bond 0.00602 ( 46) link_BETA1-4 : angle 2.35505 ( 138) link_NAG-ASN : bond 0.00323 ( 42) link_NAG-ASN : angle 2.17310 ( 126) *********************** 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 532 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 428 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 543 ASN cc_start: 0.8494 (t0) cc_final: 0.7883 (t0) REVERT: B 588 ARG cc_start: 0.8381 (tpp-160) cc_final: 0.8014 (tmm-80) REVERT: B 595 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9009 (tp) REVERT: B 657 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8842 (tm-30) REVERT: C 180 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.7539 (t0) REVERT: C 423 ILE cc_start: 0.9636 (mp) cc_final: 0.9115 (mp) REVERT: D 601 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8765 (mtpp) REVERT: E 177 TYR cc_start: 0.9027 (m-80) cc_final: 0.8743 (m-10) REVERT: G 89 MET cc_start: 0.8708 (mmm) cc_final: 0.8438 (mmm) REVERT: I 38 ARG cc_start: 0.8679 (ptt180) cc_final: 0.8414 (ptt180) REVERT: I 46 GLU cc_start: 0.7771 (tt0) cc_final: 0.7399 (tt0) REVERT: I 86 ASP cc_start: 0.8710 (m-30) cc_final: 0.8497 (m-30) REVERT: L 27 GLN cc_start: 0.8306 (tp40) cc_final: 0.7886 (tm-30) REVERT: L 28 ASP cc_start: 0.8367 (t0) cc_final: 0.8006 (t0) REVERT: L 73 LEU cc_start: 0.7693 (pp) cc_final: 0.7067 (tt) outliers start: 104 outliers final: 60 residues processed: 502 average time/residue: 0.1432 time to fit residues: 116.5619 Evaluate side-chains 450 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 388 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 465 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 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 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP 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 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 75 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 110 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 242 VAL Chi-restraints excluded: chain E residue 270 VAL 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 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 113 SER 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 90 VAL 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 97 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 215 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3020 r_free = 0.3020 target = 0.070107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.058453 restraints weight = 66217.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.060431 restraints weight = 32447.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.061762 restraints weight = 20127.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.062616 restraints weight = 14487.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.063251 restraints weight = 11573.312| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22630 Z= 0.272 Angle : 0.733 10.610 30965 Z= 0.344 Chirality : 0.047 0.391 3736 Planarity : 0.004 0.035 3751 Dihedral : 10.068 78.161 4941 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 6.41 % Allowed : 29.84 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.17), residues: 2588 helix: 2.02 (0.28), residues: 375 sheet: 0.05 (0.21), residues: 667 loop : -0.88 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 42 TYR 0.019 0.002 TYR E 217 PHE 0.013 0.002 PHE N 91 TRP 0.023 0.002 TRP E 479 HIS 0.005 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00619 (22487) covalent geometry : angle 0.69516 (30577) SS BOND : bond 0.00393 ( 41) SS BOND : angle 0.82971 ( 82) hydrogen bonds : bond 0.03785 ( 773) hydrogen bonds : angle 5.32105 ( 2013) link_ALPHA1-2 : bond 0.00357 ( 1) link_ALPHA1-2 : angle 2.80160 ( 3) link_ALPHA1-3 : bond 0.00774 ( 7) link_ALPHA1-3 : angle 2.59779 ( 21) link_ALPHA1-6 : bond 0.00501 ( 6) link_ALPHA1-6 : angle 2.14436 ( 18) link_BETA1-4 : bond 0.00555 ( 46) link_BETA1-4 : angle 2.43109 ( 138) link_NAG-ASN : bond 0.00540 ( 42) link_NAG-ASN : angle 2.40834 ( 126) *********************** 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 530 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 385 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 275 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 378 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7008 (t) REVERT: B 530 MET cc_start: 0.8330 (mmt) cc_final: 0.7789 (mmm) REVERT: B 543 ASN cc_start: 0.8554 (t0) cc_final: 0.7903 (t0) REVERT: B 588 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.8049 (tmm-80) REVERT: B 595 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9066 (tp) REVERT: B 657 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8857 (tm-30) REVERT: C 178 ARG cc_start: 0.8448 (tpt170) cc_final: 0.8109 (tpt170) REVERT: C 180 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.7707 (t0) REVERT: C 304 ARG cc_start: 0.9562 (OUTLIER) cc_final: 0.8116 (ptm-80) REVERT: C 423 ILE cc_start: 0.9681 (mp) cc_final: 0.9233 (mp) REVERT: C 475 MET cc_start: 0.9573 (mmm) cc_final: 0.9355 (mmm) REVERT: D 530 MET cc_start: 0.8520 (mpp) cc_final: 0.7872 (mpp) REVERT: F 577 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8070 (tp40) REVERT: H 72 ASP cc_start: 0.8685 (t0) cc_final: 0.8250 (t0) REVERT: I 38 ARG cc_start: 0.8736 (ptt180) cc_final: 0.8474 (ptt180) REVERT: I 46 GLU cc_start: 0.7933 (tt0) cc_final: 0.7505 (tt0) REVERT: I 71 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8675 (pmt170) REVERT: J 46 GLU cc_start: 0.8077 (tp30) cc_final: 0.7837 (tp30) REVERT: L 27 GLN cc_start: 0.8350 (tp40) cc_final: 0.7735 (tm-30) REVERT: L 28 ASP cc_start: 0.8400 (t0) cc_final: 0.8050 (t0) REVERT: M 35 TRP cc_start: 0.9133 (m100) cc_final: 0.8596 (m100) outliers start: 145 outliers final: 91 residues processed: 495 average time/residue: 0.1424 time to fit residues: 114.6908 Evaluate side-chains 470 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 371 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 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 201 ILE 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 275 GLU 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 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 583 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 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 278 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 648 GLU 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 109 ILE 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 236 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 290 THR 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 587 LEU 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 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 H residue 98 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain J residue 29 THR 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 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 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 33 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 180 optimal weight: 0.0020 chunk 213 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN 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 = 0.3046 r_free = 0.3046 target = 0.071364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.059732 restraints weight = 65208.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.061746 restraints weight = 31847.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.063098 restraints weight = 19620.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063959 restraints weight = 14069.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064588 restraints weight = 11188.675| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1307 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= 0.179 Angle : 0.680 9.836 30965 Z= 0.319 Chirality : 0.046 0.398 3736 Planarity : 0.003 0.035 3751 Dihedral : 9.152 70.206 4941 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 6.01 % Allowed : 30.28 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2588 helix: 2.10 (0.28), residues: 375 sheet: 0.00 (0.20), residues: 745 loop : -0.81 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 273 TYR 0.023 0.002 TYR F 586 PHE 0.010 0.001 PHE C 391 TRP 0.037 0.001 TRP C 69 HIS 0.005 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00410 (22487) covalent geometry : angle 0.64527 (30577) SS BOND : bond 0.00324 ( 41) SS BOND : angle 0.73936 ( 82) hydrogen bonds : bond 0.03499 ( 773) hydrogen bonds : angle 5.15492 ( 2013) link_ALPHA1-2 : bond 0.00644 ( 1) link_ALPHA1-2 : angle 2.42565 ( 3) link_ALPHA1-3 : bond 0.00785 ( 7) link_ALPHA1-3 : angle 2.53255 ( 21) link_ALPHA1-6 : bond 0.00523 ( 6) link_ALPHA1-6 : angle 1.98528 ( 18) link_BETA1-4 : bond 0.00567 ( 46) link_BETA1-4 : angle 2.26412 ( 138) link_NAG-ASN : bond 0.00368 ( 42) link_NAG-ASN : angle 2.23627 ( 126) *********************** 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 543 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 407 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: A 378 CYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7017 (t) REVERT: B 530 MET cc_start: 0.8237 (mmt) cc_final: 0.7705 (mmm) REVERT: B 543 ASN cc_start: 0.8585 (t0) cc_final: 0.7955 (t0) REVERT: B 588 ARG cc_start: 0.8385 (tpp-160) cc_final: 0.7993 (tmm-80) REVERT: B 595 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9056 (tp) REVERT: B 657 GLU cc_start: 0.9312 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 178 ARG cc_start: 0.8457 (tpt170) cc_final: 0.8108 (tpt170) REVERT: C 180 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.7710 (t0) REVERT: C 423 ILE cc_start: 0.9677 (mp) cc_final: 0.9214 (mp) REVERT: C 486 TYR cc_start: 0.9458 (m-80) cc_final: 0.9115 (m-80) REVERT: E 69 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.7655 (m100) REVERT: E 104 MET cc_start: 0.9113 (tmm) cc_final: 0.8689 (ttp) REVERT: E 177 TYR cc_start: 0.9062 (m-80) cc_final: 0.8751 (m-10) REVERT: E 304 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8309 (ttp80) REVERT: G 89 MET cc_start: 0.8605 (mmm) cc_final: 0.8328 (mmm) REVERT: I 38 ARG cc_start: 0.8700 (ptt180) cc_final: 0.8406 (ptt180) REVERT: I 46 GLU cc_start: 0.7944 (tt0) cc_final: 0.7529 (tt0) REVERT: I 71 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8694 (pmt170) REVERT: I 86 ASP cc_start: 0.8794 (m-30) cc_final: 0.8545 (m-30) REVERT: J 46 GLU cc_start: 0.8021 (tp30) cc_final: 0.7770 (tp30) REVERT: L 27 GLN cc_start: 0.8261 (tp40) cc_final: 0.7809 (tm-30) REVERT: L 28 ASP cc_start: 0.8354 (t0) cc_final: 0.7891 (t0) REVERT: M 35 TRP cc_start: 0.9145 (m100) cc_final: 0.8564 (m100) outliers start: 136 outliers final: 88 residues processed: 510 average time/residue: 0.1476 time to fit residues: 121.2316 Evaluate side-chains 486 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 391 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 100 MET 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 201 ILE Chi-restraints excluded: chain A residue 208 VAL 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 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 573 ILE Chi-restraints excluded: chain B residue 581 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 115 SER 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 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 345 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 CYS 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 606 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 69 TRP 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 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 304 ARG 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 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 24 LYS 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 71 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 85 ASP 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 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 90 VAL 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 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 60 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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** E 428 GLN F 577 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061382 restraints weight = 64825.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.063400 restraints weight = 31832.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.064748 restraints weight = 19704.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.065662 restraints weight = 14118.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066240 restraints weight = 11142.518| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22630 Z= 0.133 Angle : 0.657 10.412 30965 Z= 0.308 Chirality : 0.046 0.409 3736 Planarity : 0.003 0.035 3751 Dihedral : 8.467 73.963 4941 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 5.04 % Allowed : 31.26 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.17), residues: 2588 helix: 2.19 (0.28), residues: 375 sheet: 0.15 (0.19), residues: 778 loop : -0.78 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 273 TYR 0.019 0.001 TYR F 586 PHE 0.013 0.001 PHE M 62 TRP 0.022 0.001 TRP C 69 HIS 0.004 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00307 (22487) covalent geometry : angle 0.62530 (30577) SS BOND : bond 0.00296 ( 41) SS BOND : angle 0.72812 ( 82) hydrogen bonds : bond 0.03276 ( 773) hydrogen bonds : angle 5.04254 ( 2013) link_ALPHA1-2 : bond 0.00830 ( 1) link_ALPHA1-2 : angle 2.19592 ( 3) link_ALPHA1-3 : bond 0.00844 ( 7) link_ALPHA1-3 : angle 2.46585 ( 21) link_ALPHA1-6 : bond 0.00588 ( 6) link_ALPHA1-6 : angle 1.79045 ( 18) link_BETA1-4 : bond 0.00578 ( 46) link_BETA1-4 : angle 2.14561 ( 138) link_NAG-ASN : bond 0.00304 ( 42) link_NAG-ASN : angle 2.08978 ( 126) *********************** 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 548 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 434 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: A 378 CYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6887 (t) REVERT: B 543 ASN cc_start: 0.8545 (t0) cc_final: 0.8006 (t0) REVERT: B 588 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.8036 (tmm-80) REVERT: B 595 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8998 (tp) REVERT: B 657 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8829 (tm-30) REVERT: C 150 MET cc_start: 0.9083 (mmp) cc_final: 0.8604 (mmt) REVERT: C 178 ARG cc_start: 0.8384 (tpt170) cc_final: 0.8024 (tpt170) REVERT: C 180 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.7599 (t0) REVERT: C 321 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: C 423 ILE cc_start: 0.9684 (mp) cc_final: 0.9247 (mp) REVERT: C 486 TYR cc_start: 0.9383 (m-80) cc_final: 0.9102 (m-80) REVERT: D 601 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8656 (mmmm) REVERT: E 104 MET cc_start: 0.9076 (tmm) cc_final: 0.8650 (ttp) REVERT: E 177 TYR cc_start: 0.8967 (m-80) cc_final: 0.8681 (m-10) REVERT: F 586 TYR cc_start: 0.9415 (t80) cc_final: 0.9176 (t80) REVERT: I 71 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8627 (pmt170) REVERT: J 46 GLU cc_start: 0.7919 (tp30) cc_final: 0.7689 (tp30) REVERT: L 27 GLN cc_start: 0.8226 (tp40) cc_final: 0.7758 (tm-30) REVERT: L 28 ASP cc_start: 0.8262 (t0) cc_final: 0.7784 (t0) REVERT: M 35 TRP cc_start: 0.9008 (m100) cc_final: 0.8495 (m100) REVERT: N 61 ARG cc_start: 0.8496 (mtp180) cc_final: 0.8121 (mtm110) outliers start: 114 outliers final: 81 residues processed: 517 average time/residue: 0.1478 time to fit residues: 122.7905 Evaluate side-chains 488 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 401 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET 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 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 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 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 181 VAL 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 321 ASP 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 593 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 648 GLU 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 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 463 SER 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 58 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 35 LEU 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 90 VAL 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 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 11 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 B 651 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 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 = 0.3025 r_free = 0.3025 target = 0.070355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.058644 restraints weight = 66174.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.060625 restraints weight = 32618.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061933 restraints weight = 20259.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.062856 restraints weight = 14641.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.063434 restraints weight = 11603.999| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22630 Z= 0.265 Angle : 0.733 12.410 30965 Z= 0.345 Chirality : 0.047 0.386 3736 Planarity : 0.004 0.036 3751 Dihedral : 8.548 76.974 4941 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.41 % Favored : 93.51 % Rotamer: Outliers : 5.48 % Allowed : 31.92 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.17), residues: 2588 helix: 2.04 (0.28), residues: 375 sheet: 0.05 (0.20), residues: 741 loop : -0.88 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.019 0.002 TYR E 217 PHE 0.017 0.002 PHE N 91 TRP 0.039 0.002 TRP C 69 HIS 0.005 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00604 (22487) covalent geometry : angle 0.69933 (30577) SS BOND : bond 0.00394 ( 41) SS BOND : angle 0.84322 ( 82) hydrogen bonds : bond 0.03566 ( 773) hydrogen bonds : angle 5.14872 ( 2013) link_ALPHA1-2 : bond 0.00470 ( 1) link_ALPHA1-2 : angle 2.61648 ( 3) link_ALPHA1-3 : bond 0.00807 ( 7) link_ALPHA1-3 : angle 2.59380 ( 21) link_ALPHA1-6 : bond 0.00544 ( 6) link_ALPHA1-6 : angle 1.94555 ( 18) link_BETA1-4 : bond 0.00558 ( 46) link_BETA1-4 : angle 2.24165 ( 138) link_NAG-ASN : bond 0.00529 ( 42) link_NAG-ASN : angle 2.34116 ( 126) *********************** 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 507 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 383 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: A 378 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6960 (t) REVERT: B 530 MET cc_start: 0.8334 (mmt) cc_final: 0.7934 (mmm) REVERT: B 543 ASN cc_start: 0.8603 (t0) cc_final: 0.8022 (t0) REVERT: B 588 ARG cc_start: 0.8398 (tpp-160) cc_final: 0.8046 (tmm-80) REVERT: B 595 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9058 (tp) REVERT: B 657 GLU cc_start: 0.9299 (tm-30) cc_final: 0.8849 (tm-30) REVERT: C 150 MET cc_start: 0.9174 (mmp) cc_final: 0.8765 (mmt) REVERT: C 178 ARG cc_start: 0.8473 (tpt170) cc_final: 0.8099 (tpt170) REVERT: C 180 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.7778 (t0) REVERT: C 423 ILE cc_start: 0.9691 (OUTLIER) cc_final: 0.9247 (mp) REVERT: C 486 TYR cc_start: 0.9467 (m-80) cc_final: 0.9153 (m-80) REVERT: D 601 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8866 (mmmm) REVERT: E 69 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.7622 (m100) REVERT: E 177 TYR cc_start: 0.9109 (m-80) cc_final: 0.8808 (m-10) REVERT: E 304 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8305 (ttp80) REVERT: E 377 ASN cc_start: 0.9329 (t0) cc_final: 0.9113 (t0) REVERT: H 72 ASP cc_start: 0.8752 (t0) cc_final: 0.8234 (t0) REVERT: I 38 ARG cc_start: 0.8681 (ptt180) cc_final: 0.8479 (ptt180) REVERT: I 46 GLU cc_start: 0.7841 (tt0) cc_final: 0.7518 (tt0) REVERT: I 71 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8673 (pmt170) REVERT: I 83 LYS cc_start: 0.9180 (mmtp) cc_final: 0.8927 (mmmm) REVERT: J 46 GLU cc_start: 0.8058 (tp30) cc_final: 0.7792 (tp30) REVERT: L 27 GLN cc_start: 0.8302 (tp40) cc_final: 0.7802 (tm-30) REVERT: L 28 ASP cc_start: 0.8369 (t0) cc_final: 0.7923 (t0) REVERT: M 35 TRP cc_start: 0.9155 (m100) cc_final: 0.8537 (m100) outliers start: 124 outliers final: 97 residues processed: 482 average time/residue: 0.1459 time to fit residues: 113.7427 Evaluate side-chains 485 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 380 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 106 THR 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 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 573 ILE 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 115 SER 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 181 VAL 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 236 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 373 THR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 587 LEU 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 69 TRP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 ARG 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 520 LEU 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 642 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 30 ASN 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 71 ARG Chi-restraints excluded: chain I residue 85 ASP 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 67 ILE 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 90 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 135 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.061782 restraints weight = 64625.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.063843 restraints weight = 31549.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.065201 restraints weight = 19400.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.066139 restraints weight = 13911.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.066729 restraints weight = 10963.233| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1612 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= 0.124 Angle : 0.678 14.211 30965 Z= 0.318 Chirality : 0.046 0.415 3736 Planarity : 0.003 0.034 3751 Dihedral : 8.021 76.983 4938 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 4.11 % Allowed : 32.85 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.17), residues: 2588 helix: 2.13 (0.28), residues: 375 sheet: 0.05 (0.19), residues: 792 loop : -0.76 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 62 TYR 0.019 0.002 TYR F 586 PHE 0.017 0.001 PHE G 98 TRP 0.032 0.001 TRP C 69 HIS 0.004 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00284 (22487) covalent geometry : angle 0.64982 (30577) SS BOND : bond 0.00312 ( 41) SS BOND : angle 0.80721 ( 82) hydrogen bonds : bond 0.03227 ( 773) hydrogen bonds : angle 4.99466 ( 2013) link_ALPHA1-2 : bond 0.00954 ( 1) link_ALPHA1-2 : angle 2.06449 ( 3) link_ALPHA1-3 : bond 0.00872 ( 7) link_ALPHA1-3 : angle 2.35082 ( 21) link_ALPHA1-6 : bond 0.00575 ( 6) link_ALPHA1-6 : angle 1.68817 ( 18) link_BETA1-4 : bond 0.00591 ( 46) link_BETA1-4 : angle 2.04868 ( 138) link_NAG-ASN : bond 0.00278 ( 42) link_NAG-ASN : angle 2.04686 ( 126) *********************** 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 521 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 428 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: A 378 CYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6932 (t) REVERT: B 543 ASN cc_start: 0.8562 (t0) cc_final: 0.7983 (t0) REVERT: B 588 ARG cc_start: 0.8318 (tpp-160) cc_final: 0.8035 (tmm-80) REVERT: B 595 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9010 (tp) REVERT: B 657 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8824 (tm-30) REVERT: C 150 MET cc_start: 0.9107 (mmp) cc_final: 0.8750 (mmt) REVERT: C 178 ARG cc_start: 0.8404 (tpt170) cc_final: 0.7948 (tpt170) REVERT: C 180 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.7654 (t0) REVERT: C 423 ILE cc_start: 0.9679 (mp) cc_final: 0.9296 (mp) REVERT: C 486 TYR cc_start: 0.9371 (m-80) cc_final: 0.9040 (m-80) REVERT: D 601 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8790 (mmmm) REVERT: E 177 TYR cc_start: 0.8969 (m-80) cc_final: 0.8690 (m-10) REVERT: E 377 ASN cc_start: 0.9265 (t0) cc_final: 0.8991 (t0) REVERT: F 577 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: F 653 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8806 (tm-30) REVERT: G 90 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8303 (pp30) REVERT: I 46 GLU cc_start: 0.7793 (tt0) cc_final: 0.7567 (tt0) REVERT: I 71 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8653 (pmt170) REVERT: I 79 TYR cc_start: 0.9160 (m-10) cc_final: 0.8939 (m-10) REVERT: I 83 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8913 (mmmm) REVERT: J 35 GLU cc_start: 0.7593 (tp30) cc_final: 0.7259 (tp30) REVERT: J 46 GLU cc_start: 0.7935 (tp30) cc_final: 0.7685 (tp30) REVERT: L 27 GLN cc_start: 0.8225 (tp40) cc_final: 0.7762 (tm-30) REVERT: L 28 ASP cc_start: 0.8289 (t0) cc_final: 0.7814 (t0) REVERT: M 35 TRP cc_start: 0.9015 (m100) cc_final: 0.8442 (m100) REVERT: N 61 ARG cc_start: 0.8491 (mtp180) cc_final: 0.8132 (mtm110) outliers start: 93 outliers final: 81 residues processed: 501 average time/residue: 0.1480 time to fit residues: 119.3280 Evaluate side-chains 494 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 406 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR 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 162 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 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 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 115 SER 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 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 357 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL 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 645 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 147 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 270 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 463 SER 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 636 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain H residue 17 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 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 51 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 90 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 229 optimal weight: 8.9990 chunk 47 optimal weight: 0.3980 chunk 135 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 0.0370 chunk 48 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- 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 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 = 0.3097 r_free = 0.3097 target = 0.073846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.062147 restraints weight = 64715.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.064186 restraints weight = 31653.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.065568 restraints weight = 19553.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.066451 restraints weight = 13990.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067106 restraints weight = 11122.408| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1672 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= 0.124 Angle : 0.681 15.408 30965 Z= 0.318 Chirality : 0.045 0.413 3736 Planarity : 0.003 0.033 3751 Dihedral : 7.764 76.272 4938 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 4.29 % Allowed : 33.24 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2588 helix: 2.14 (0.28), residues: 375 sheet: 0.12 (0.19), residues: 795 loop : -0.73 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 66 TYR 0.020 0.002 TYR K 100C PHE 0.013 0.001 PHE N 91 TRP 0.034 0.001 TRP C 69 HIS 0.004 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00289 (22487) covalent geometry : angle 0.65391 (30577) SS BOND : bond 0.00304 ( 41) SS BOND : angle 0.78194 ( 82) hydrogen bonds : bond 0.03173 ( 773) hydrogen bonds : angle 4.92740 ( 2013) link_ALPHA1-2 : bond 0.00935 ( 1) link_ALPHA1-2 : angle 2.04185 ( 3) link_ALPHA1-3 : bond 0.00845 ( 7) link_ALPHA1-3 : angle 2.29131 ( 21) link_ALPHA1-6 : bond 0.00572 ( 6) link_ALPHA1-6 : angle 1.64338 ( 18) link_BETA1-4 : bond 0.00578 ( 46) link_BETA1-4 : angle 2.02167 ( 138) link_NAG-ASN : bond 0.00269 ( 42) link_NAG-ASN : angle 2.02235 ( 126) *********************** 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 521 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 424 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 378 CYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6958 (t) REVERT: B 543 ASN cc_start: 0.8561 (t0) cc_final: 0.8036 (t0) REVERT: B 588 ARG cc_start: 0.8324 (tpp-160) cc_final: 0.8014 (tmm-80) REVERT: B 595 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9012 (tp) REVERT: B 657 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 150 MET cc_start: 0.9118 (mmp) cc_final: 0.8321 (tpp) REVERT: C 178 ARG cc_start: 0.8410 (tpt170) cc_final: 0.7983 (tpt170) REVERT: C 180 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.7644 (t0) REVERT: C 423 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9312 (mp) REVERT: C 486 TYR cc_start: 0.9351 (m-80) cc_final: 0.9024 (m-80) REVERT: D 530 MET cc_start: 0.8478 (tpp) cc_final: 0.7887 (mpp) REVERT: D 601 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8770 (mmmm) REVERT: D 647 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8161 (mt-10) REVERT: E 177 TYR cc_start: 0.8967 (m-80) cc_final: 0.8681 (m-10) REVERT: E 375 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8716 (p) REVERT: E 377 ASN cc_start: 0.9282 (t0) cc_final: 0.8999 (t0) REVERT: F 577 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: G 45 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7869 (mm110) REVERT: I 46 GLU cc_start: 0.7757 (tt0) cc_final: 0.7460 (tt0) REVERT: I 71 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8596 (pmt170) REVERT: I 79 TYR cc_start: 0.9156 (m-10) cc_final: 0.8937 (m-10) REVERT: I 83 LYS cc_start: 0.9124 (mmtp) cc_final: 0.8913 (mmmm) REVERT: J 35 GLU cc_start: 0.7617 (tp30) cc_final: 0.7253 (tp30) REVERT: J 46 GLU cc_start: 0.7922 (tp30) cc_final: 0.7701 (tp30) REVERT: K 100 TYR cc_start: 0.8661 (m-10) cc_final: 0.8333 (m-10) REVERT: L 27 GLN cc_start: 0.8243 (tp40) cc_final: 0.7759 (tm-30) REVERT: L 28 ASP cc_start: 0.8286 (t0) cc_final: 0.7791 (t0) REVERT: M 35 TRP cc_start: 0.9011 (m100) cc_final: 0.8445 (m100) REVERT: N 61 ARG cc_start: 0.8499 (mtp180) cc_final: 0.8130 (mtm110) outliers start: 97 outliers final: 79 residues processed: 499 average time/residue: 0.1492 time to fit residues: 118.8816 Evaluate side-chains 493 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 406 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 SER 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 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 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 115 SER 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 278 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 423 ILE 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 645 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 270 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 570 VAL Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 608 VAL 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 24 LYS Chi-restraints excluded: chain G residue 30 ASN 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 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 51 VAL 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 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR 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 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 140 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 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 = 0.3063 r_free = 0.3063 target = 0.072196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.060532 restraints weight = 65366.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.062540 restraints weight = 32065.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063931 restraints weight = 19834.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.064786 restraints weight = 14113.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.065436 restraints weight = 11274.791| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 0.073 22630 Z= 0.192 Angle : 0.721 16.675 30965 Z= 0.334 Chirality : 0.046 0.400 3736 Planarity : 0.004 0.034 3751 Dihedral : 7.793 75.380 4938 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.13 % Rotamer: Outliers : 4.29 % Allowed : 33.24 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2588 helix: 2.08 (0.29), residues: 375 sheet: 0.03 (0.19), residues: 828 loop : -0.78 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 66 TYR 0.024 0.002 TYR F 586 PHE 0.013 0.001 PHE N 91 TRP 0.052 0.002 TRP L 35 HIS 0.004 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00445 (22487) covalent geometry : angle 0.69262 (30577) SS BOND : bond 0.00344 ( 41) SS BOND : angle 0.80523 ( 82) hydrogen bonds : bond 0.03319 ( 773) hydrogen bonds : angle 4.95273 ( 2013) link_ALPHA1-2 : bond 0.00700 ( 1) link_ALPHA1-2 : angle 2.26678 ( 3) link_ALPHA1-3 : bond 0.00783 ( 7) link_ALPHA1-3 : angle 2.37967 ( 21) link_ALPHA1-6 : bond 0.00537 ( 6) link_ALPHA1-6 : angle 1.73318 ( 18) link_BETA1-4 : bond 0.00554 ( 46) link_BETA1-4 : angle 2.08489 ( 138) link_NAG-ASN : bond 0.00357 ( 42) link_NAG-ASN : angle 2.16294 ( 126) ********************** 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 501 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 404 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: A 378 CYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6888 (t) REVERT: B 543 ASN cc_start: 0.8589 (t0) cc_final: 0.8007 (t0) REVERT: B 588 ARG cc_start: 0.8350 (tpp-160) cc_final: 0.8036 (tmm-80) REVERT: B 595 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9022 (tp) REVERT: B 657 GLU cc_start: 0.9300 (tm-30) cc_final: 0.8828 (tm-30) REVERT: C 150 MET cc_start: 0.9147 (mmp) cc_final: 0.8390 (tpp) REVERT: C 178 ARG cc_start: 0.8449 (tpt170) cc_final: 0.8031 (tpt170) REVERT: C 180 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.7673 (t0) REVERT: C 423 ILE cc_start: 0.9694 (OUTLIER) cc_final: 0.9322 (mp) REVERT: C 486 TYR cc_start: 0.9406 (m-80) cc_final: 0.9140 (m-80) REVERT: D 530 MET cc_start: 0.8583 (tpp) cc_final: 0.8005 (mpp) REVERT: D 601 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8840 (mmmm) REVERT: E 177 TYR cc_start: 0.9039 (m-80) cc_final: 0.8750 (m-10) REVERT: E 377 ASN cc_start: 0.9308 (t0) cc_final: 0.9062 (t0) REVERT: F 577 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: F 653 GLN cc_start: 0.9098 (tm130) cc_final: 0.8841 (tm-30) REVERT: G 45 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7815 (mm110) REVERT: G 90 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8862 (pp30) REVERT: H 72 ASP cc_start: 0.8732 (t0) cc_final: 0.8215 (t0) REVERT: I 46 GLU cc_start: 0.7789 (tt0) cc_final: 0.7549 (tt0) REVERT: I 71 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8585 (pmt170) REVERT: I 83 LYS cc_start: 0.9156 (mmtp) cc_final: 0.8930 (mmmm) REVERT: J 35 GLU cc_start: 0.7646 (tp30) cc_final: 0.7435 (tp30) REVERT: J 46 GLU cc_start: 0.7939 (tp30) cc_final: 0.7714 (tp30) REVERT: K 100 TYR cc_start: 0.8659 (m-10) cc_final: 0.8395 (m-10) REVERT: L 27 GLN cc_start: 0.8285 (tp40) cc_final: 0.7813 (tm-30) REVERT: L 28 ASP cc_start: 0.8294 (t0) cc_final: 0.7810 (t0) REVERT: N 61 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8096 (mtm110) outliers start: 97 outliers final: 82 residues processed: 482 average time/residue: 0.1435 time to fit residues: 112.0685 Evaluate side-chains 489 residues out of total 2309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 399 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 162 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 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 115 SER 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 423 ILE 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 593 LEU Chi-restraints excluded: chain D residue 645 LEU 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 147 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 270 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 570 VAL Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 608 VAL 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 24 LYS Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 90 GLN 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 64 GLN Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain J residue 51 VAL 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 100 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 208 optimal weight: 0.0770 chunk 45 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 37 HIS ** 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 = 0.3091 r_free = 0.3091 target = 0.073561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061891 restraints weight = 64716.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063938 restraints weight = 31624.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.065309 restraints weight = 19460.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066185 restraints weight = 13917.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.066843 restraints weight = 11073.207| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1717 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= 0.129 Angle : 0.693 15.789 30965 Z= 0.322 Chirality : 0.046 0.409 3736 Planarity : 0.003 0.033 3751 Dihedral : 7.637 73.973 4938 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 3.93 % Allowed : 33.73 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.17), residues: 2588 helix: 2.07 (0.28), residues: 375 sheet: 0.10 (0.19), residues: 789 loop : -0.71 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 42 TYR 0.023 0.002 TYR F 643 PHE 0.018 0.001 PHE L 91 TRP 0.051 0.002 TRP L 35 HIS 0.004 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00300 (22487) covalent geometry : angle 0.66663 (30577) SS BOND : bond 0.00318 ( 41) SS BOND : angle 0.78485 ( 82) hydrogen bonds : bond 0.03213 ( 773) hydrogen bonds : angle 4.91009 ( 2013) link_ALPHA1-2 : bond 0.00902 ( 1) link_ALPHA1-2 : angle 2.06336 ( 3) link_ALPHA1-3 : bond 0.00816 ( 7) link_ALPHA1-3 : angle 2.27846 ( 21) link_ALPHA1-6 : bond 0.00580 ( 6) link_ALPHA1-6 : angle 1.61628 ( 18) link_BETA1-4 : bond 0.00577 ( 46) link_BETA1-4 : angle 2.00884 ( 138) link_NAG-ASN : bond 0.00274 ( 42) link_NAG-ASN : angle 2.03622 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3699.21 seconds wall clock time: 65 minutes 27.67 seconds (3927.67 seconds total)