Starting phenix.real_space_refine on Sat Jun 21 17:14:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mib_48287/06_2025/9mib_48287.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mib_48287/06_2025/9mib_48287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mib_48287/06_2025/9mib_48287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mib_48287/06_2025/9mib_48287.map" model { file = "/net/cci-nas-00/data/ceres_data/9mib_48287/06_2025/9mib_48287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mib_48287/06_2025/9mib_48287.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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 156 5.16 5 C 15813 2.51 5 N 4233 2.21 5 O 5064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25266 Number of models: 1 Model: "" Number of chains: 54 Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3500 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "L" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3500 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "K" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Chain: "O" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3500 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "P" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "R" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "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: 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: "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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "j" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: 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: 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: "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: 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: "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: "A" 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: "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: 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: "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 Time building chain proxies: 16.30, per 1000 atoms: 0.65 Number of scatterers: 25266 At special positions: 0 Unit cell: (138.543, 145.78, 150.949, 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 156 16.00 O 5064 8.00 N 4233 7.00 C 15813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=1.49 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=2.03 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=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 100C" distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=1.49 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=2.07 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 98 " - pdb=" SG CYS K 100C" distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=1.49 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.08 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 98 " - pdb=" SG CYS P 100C" distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 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 ALPHA1-3 " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 5 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA Y 3 " - " MAN Y 6 " " BMA i 3 " - " MAN i 6 " " BMA s 3 " - " MAN s 6 " BETA1-4 " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 339 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 301 " " NAG a 1 " - " ASN A 332 " " NAG b 1 " - " ASN A 363 " " NAG c 1 " - " ASN C 160 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 295 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN C 392 " " NAG h 1 " - " ASN C 448 " " NAG i 1 " - " ASN C 262 " " NAG j 1 " - " ASN C 301 " " NAG k 1 " - " ASN C 332 " " NAG l 1 " - " ASN C 363 " " NAG m 1 " - " ASN E 160 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 295 " " NAG p 1 " - " ASN E 88 " " NAG q 1 " - " ASN E 392 " " NAG r 1 " - " ASN E 448 " " NAG s 1 " - " ASN E 262 " " NAG t 1 " - " ASN E 301 " " NAG u 1 " - " ASN E 332 " " NAG v 1 " - " ASN E 363 " Time building additional restraints: 7.79 Conformation dependent library (CDL) restraints added in 3.2 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 69 sheets defined 17.5% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.563A pdb=" N LYS G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.605A pdb=" N THR G 87 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.925A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.544A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.790A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.903A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.500A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.835A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.240A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.563A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.604A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.925A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.545A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.790A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.903A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.501A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 649 removed outlier: 3.834A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.240A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.563A pdb=" N LYS O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.604A pdb=" N THR O 87 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.925A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.544A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.789A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.903A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.500A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.835A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.240A pdb=" N ILE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.005A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.005A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.423A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.200A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.821A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.434A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AB3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.261A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.245A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.172A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.275A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.830A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 17 through 20 Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 9 through 12 removed outlier: 6.423A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'M' and resid 18 through 24 Processing sheet with id=AD3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.201A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.821A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.434A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AD8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD9, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.260A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.245A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.172A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.275A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.829A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 17 through 20 Processing sheet with id=AE8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'O' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE O 102 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.424A pdb=" N TRP Q 35 " --> pdb=" O MET Q 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'Q' and resid 18 through 24 Processing sheet with id=AF8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.201A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.821A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.434A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AG3, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AG4, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AG5, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.261A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.245A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 271 through 274 removed outlier: 11.172A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AG9, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AH1, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.276A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.829A pdb=" N TYR P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 17 through 20 Processing sheet with id=AH4, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 2673 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: 11.42 Time building geometry restraints manager: 9.03 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: 7830 1.34 - 1.46: 6621 1.46 - 1.59: 11124 1.59 - 1.71: 3 1.71 - 1.83: 216 Bond restraints: 25794 Sorted by residual: bond pdb=" C ASN F 618 " pdb=" N LEU F 619 " ideal model delta sigma weight residual 1.335 1.217 0.118 1.30e-02 5.92e+03 8.27e+01 bond pdb=" C ASN B 618 " pdb=" N LEU B 619 " ideal model delta sigma weight residual 1.335 1.217 0.118 1.30e-02 5.92e+03 8.25e+01 bond pdb=" C ASN D 618 " pdb=" N LEU D 619 " ideal model delta sigma weight residual 1.335 1.217 0.118 1.30e-02 5.92e+03 8.21e+01 bond pdb=" C ASN C 392 " pdb=" N SER C 393 " ideal model delta sigma weight residual 1.330 1.241 0.089 1.22e-02 6.72e+03 5.36e+01 bond pdb=" C ASN A 392 " pdb=" N SER A 393 " ideal model delta sigma weight residual 1.330 1.241 0.089 1.22e-02 6.72e+03 5.29e+01 ... (remaining 25789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 33227 1.87 - 3.74: 1327 3.74 - 5.61: 338 5.61 - 7.48: 91 7.48 - 9.35: 18 Bond angle restraints: 35001 Sorted by residual: angle pdb=" C ASN D 618 " pdb=" N LEU D 619 " pdb=" CA LEU D 619 " ideal model delta sigma weight residual 120.38 129.73 -9.35 1.37e+00 5.33e-01 4.66e+01 angle pdb=" C ASN F 618 " pdb=" N LEU F 619 " pdb=" CA LEU F 619 " ideal model delta sigma weight residual 120.38 129.73 -9.35 1.37e+00 5.33e-01 4.66e+01 angle pdb=" C ASN B 618 " pdb=" N LEU B 619 " pdb=" CA LEU B 619 " ideal model delta sigma weight residual 120.38 129.73 -9.35 1.37e+00 5.33e-01 4.65e+01 angle pdb=" CA ASN E 88 " pdb=" CB ASN E 88 " pdb=" CG ASN E 88 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.17e+01 angle pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " pdb=" CG ASN A 88 " ideal model delta sigma weight residual 112.60 119.05 -6.45 1.00e+00 1.00e+00 4.16e+01 ... (remaining 34996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.88: 15225 22.88 - 45.76: 1074 45.76 - 68.63: 204 68.63 - 91.51: 57 91.51 - 114.39: 24 Dihedral angle restraints: 16584 sinusoidal: 7770 harmonic: 8814 Sorted by residual: dihedral pdb=" CB CYS P 98 " pdb=" SG CYS P 98 " pdb=" SG CYS P 100C" pdb=" CB CYS P 100C" ideal model delta sinusoidal sigma weight residual 93.00 162.74 -69.74 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS H 98 " pdb=" SG CYS H 98 " pdb=" SG CYS H 100C" pdb=" CB CYS H 100C" ideal model delta sinusoidal sigma weight residual 93.00 162.73 -69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS K 98 " pdb=" SG CYS K 98 " pdb=" SG CYS K 100C" pdb=" CB CYS K 100C" ideal model delta sinusoidal sigma weight residual 93.00 162.73 -69.73 1 1.00e+01 1.00e-02 6.27e+01 ... (remaining 16581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 4001 0.129 - 0.258: 134 0.258 - 0.386: 8 0.386 - 0.515: 3 0.515 - 0.644: 3 Chirality restraints: 4149 Sorted by residual: chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.19e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.18e+01 chirality pdb=" C1 NAG q 2 " pdb=" O4 NAG q 1 " pdb=" C2 NAG q 2 " pdb=" O5 NAG q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.13e+01 ... (remaining 4146 not shown) Planarity restraints: 4386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 18 " -0.720 9.50e-02 1.11e+02 3.24e-01 7.37e+01 pdb=" NE ARG N 18 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG N 18 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG N 18 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG N 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 18 " 0.720 9.50e-02 1.11e+02 3.24e-01 7.35e+01 pdb=" NE ARG L 18 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG L 18 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG L 18 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG L 18 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 18 " -0.720 9.50e-02 1.11e+02 3.24e-01 7.35e+01 pdb=" NE ARG R 18 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG R 18 " -0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG R 18 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG R 18 " -0.004 2.00e-02 2.50e+03 ... (remaining 4383 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 761 2.69 - 3.24: 22591 3.24 - 3.79: 39448 3.79 - 4.35: 56363 4.35 - 4.90: 91899 Nonbonded interactions: 211062 Sorted by model distance: nonbonded pdb=" OD1 ASP C 113 " pdb=" NH1 ARG C 429 " model vdw 2.136 3.120 nonbonded pdb=" OD1 ASP E 113 " pdb=" NH1 ARG E 429 " model vdw 2.137 3.120 nonbonded pdb=" OD1 ASP A 113 " pdb=" NH1 ARG A 429 " model vdw 2.137 3.120 nonbonded pdb=" O THR Q 26 " pdb=" OD1 ASP Q 27B" model vdw 2.169 3.040 nonbonded pdb=" O THR I 26 " pdb=" OD1 ASP I 27B" model vdw 2.169 3.040 ... (remaining 211057 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'a' selection = chain 'd' selection = chain 'f' selection = chain 'k' selection = chain 'n' selection = chain 'p' selection = chain 'u' } ncs_group { reference = chain 'Y' selection = chain 'i' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 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: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 63.660 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.270 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.008 0.537 25938 Z= 0.402 Angle : 1.102 32.586 35385 Z= 0.549 Chirality : 0.057 0.644 4149 Planarity : 0.012 0.324 4341 Dihedral : 16.464 114.391 10800 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.11 % Allowed : 17.35 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3015 helix: -0.43 (0.26), residues: 432 sheet: -0.15 (0.15), residues: 1023 loop : -0.56 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 427 HIS 0.027 0.002 HIS E 173 PHE 0.020 0.002 PHE E 53 TYR 0.016 0.002 TYR H 100D ARG 0.055 0.002 ARG N 18 Details of bonding type rmsd link_NAG-ASN : bond 0.02208 ( 45) link_NAG-ASN : angle 4.79534 ( 135) link_ALPHA1-6 : bond 0.01882 ( 3) link_ALPHA1-6 : angle 3.71384 ( 9) link_BETA1-4 : bond 0.01424 ( 42) link_BETA1-4 : angle 3.62167 ( 126) link_ALPHA1-3 : bond 0.00589 ( 6) link_ALPHA1-3 : angle 1.98069 ( 18) hydrogen bonds : bond 0.12198 ( 924) hydrogen bonds : angle 6.59948 ( 2673) SS BOND : bond 0.13463 ( 48) SS BOND : angle 8.35945 ( 96) covalent geometry : bond 0.00547 (25794) covalent geometry : angle 0.94608 (35001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 406 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8610 (mmtt) REVERT: B 574 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7840 (mttm) REVERT: H 81 GLU cc_start: 0.8141 (tt0) cc_final: 0.7788 (tt0) REVERT: J 52 ASN cc_start: 0.9085 (p0) cc_final: 0.8817 (p0) REVERT: M 53 GLN cc_start: 0.8522 (mm110) cc_final: 0.8246 (mp10) REVERT: C 166 ARG cc_start: 0.7369 (mtm180) cc_final: 0.6416 (ptt90) REVERT: C 475 MET cc_start: 0.9021 (mmt) cc_final: 0.8728 (mmm) REVERT: D 584 GLU cc_start: 0.8583 (pt0) cc_final: 0.8314 (pt0) REVERT: K 46 GLU cc_start: 0.7982 (tt0) cc_final: 0.7660 (tt0) REVERT: K 69 MET cc_start: 0.8796 (mtt) cc_final: 0.8540 (mtm) REVERT: K 81 GLU cc_start: 0.8179 (tt0) cc_final: 0.7811 (tt0) REVERT: Q 79 GLN cc_start: 0.7427 (mt0) cc_final: 0.6968 (mt0) REVERT: E 475 MET cc_start: 0.8984 (mmt) cc_final: 0.8779 (mpp) REVERT: F 577 GLN cc_start: 0.8220 (mt0) cc_final: 0.8005 (mt0) REVERT: P 54 ARG cc_start: 0.8817 (mmt90) cc_final: 0.8568 (tpt170) REVERT: P 81 GLU cc_start: 0.8119 (tt0) cc_final: 0.7721 (tt0) outliers start: 3 outliers final: 0 residues processed: 406 average time/residue: 1.3634 time to fit residues: 640.6298 Evaluate side-chains 349 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 76 ASN G 82AHIS I 38 GLN A 130 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 658 GLN H 61 GLN J 3 GLN J 76 ASN M 38 GLN C 130 GLN C 173 HIS C 355 ASN C 428 GLN D 650 GLN O 3 GLN O 76 ASN O 82AHIS O 100BGLN Q 38 GLN Q 69 ASN E 130 GLN E 173 HIS E 355 ASN F 650 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141000 restraints weight = 26875.789| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.90 r_work: 0.3353 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25938 Z= 0.146 Angle : 0.662 8.577 35385 Z= 0.324 Chirality : 0.045 0.222 4149 Planarity : 0.004 0.044 4341 Dihedral : 9.665 106.494 5289 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.12 % Allowed : 17.01 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3015 helix: -0.07 (0.26), residues: 435 sheet: -0.06 (0.16), residues: 972 loop : -0.38 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 427 HIS 0.004 0.001 HIS A 173 PHE 0.013 0.001 PHE C 53 TYR 0.011 0.001 TYR L 49 ARG 0.006 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 45) link_NAG-ASN : angle 2.65586 ( 135) link_ALPHA1-6 : bond 0.01664 ( 3) link_ALPHA1-6 : angle 2.86668 ( 9) link_BETA1-4 : bond 0.00650 ( 42) link_BETA1-4 : angle 2.47331 ( 126) link_ALPHA1-3 : bond 0.00672 ( 6) link_ALPHA1-3 : angle 2.78625 ( 18) hydrogen bonds : bond 0.04155 ( 924) hydrogen bonds : angle 5.54127 ( 2673) SS BOND : bond 0.00293 ( 48) SS BOND : angle 1.43124 ( 96) covalent geometry : bond 0.00327 (25794) covalent geometry : angle 0.61764 (35001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 362 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7363 (mmm160) REVERT: B 574 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8106 (mttm) REVERT: H 54 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8800 (tpt170) REVERT: H 81 GLU cc_start: 0.8172 (tt0) cc_final: 0.7707 (tt0) REVERT: J 52 ASN cc_start: 0.9199 (p0) cc_final: 0.8896 (p0) REVERT: M 53 GLN cc_start: 0.8618 (mm110) cc_final: 0.8187 (mm110) REVERT: C 61 TYR cc_start: 0.5040 (OUTLIER) cc_final: 0.4186 (t80) REVERT: D 584 GLU cc_start: 0.8723 (pt0) cc_final: 0.8442 (pt0) REVERT: D 647 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7068 (tm-30) REVERT: K 46 GLU cc_start: 0.8055 (tt0) cc_final: 0.7736 (tt0) REVERT: K 69 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: K 81 GLU cc_start: 0.8190 (tt0) cc_final: 0.7745 (tt0) REVERT: O 23 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6649 (mmm160) REVERT: O 75 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8042 (mmtm) REVERT: E 82 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7224 (tm-30) REVERT: E 121 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8787 (mttm) REVERT: E 475 MET cc_start: 0.8938 (mmt) cc_final: 0.8489 (mpm) REVERT: F 577 GLN cc_start: 0.8455 (mt0) cc_final: 0.8221 (mt0) outliers start: 56 outliers final: 20 residues processed: 395 average time/residue: 1.2550 time to fit residues: 577.8006 Evaluate side-chains 371 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 346 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain R residue 1 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 96 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 114 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN H 61 GLN C 173 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN O 3 GLN O 100BGLN Q 69 ASN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137173 restraints weight = 26617.053| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.89 r_work: 0.3285 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25938 Z= 0.183 Angle : 0.669 8.996 35385 Z= 0.329 Chirality : 0.046 0.236 4149 Planarity : 0.004 0.033 4341 Dihedral : 8.375 102.771 5289 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.14 % Allowed : 17.08 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3015 helix: 0.29 (0.27), residues: 414 sheet: -0.03 (0.15), residues: 1014 loop : -0.30 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 427 HIS 0.007 0.001 HIS A 173 PHE 0.013 0.002 PHE A 383 TYR 0.014 0.002 TYR Q 49 ARG 0.006 0.001 ARG E 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 45) link_NAG-ASN : angle 2.45855 ( 135) link_ALPHA1-6 : bond 0.02422 ( 3) link_ALPHA1-6 : angle 3.20659 ( 9) link_BETA1-4 : bond 0.00623 ( 42) link_BETA1-4 : angle 2.15426 ( 126) link_ALPHA1-3 : bond 0.00731 ( 6) link_ALPHA1-3 : angle 2.81983 ( 18) hydrogen bonds : bond 0.04272 ( 924) hydrogen bonds : angle 5.41016 ( 2673) SS BOND : bond 0.00366 ( 48) SS BOND : angle 1.45860 ( 96) covalent geometry : bond 0.00421 (25794) covalent geometry : angle 0.63206 (35001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 367 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7252 (mmm160) REVERT: A 121 LYS cc_start: 0.9274 (mtpt) cc_final: 0.8861 (mttt) REVERT: B 574 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8176 (mttm) REVERT: H 54 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8833 (tpt170) REVERT: M 95 GLN cc_start: 0.8560 (mp-120) cc_final: 0.8165 (mm110) REVERT: C 61 TYR cc_start: 0.5106 (OUTLIER) cc_final: 0.4291 (t80) REVERT: C 84 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8727 (mp) REVERT: C 396 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8446 (mp) REVERT: C 479 TRP cc_start: 0.7629 (m-10) cc_final: 0.7337 (m-10) REVERT: K 46 GLU cc_start: 0.8200 (tt0) cc_final: 0.7908 (tt0) REVERT: K 81 GLU cc_start: 0.8287 (tt0) cc_final: 0.7821 (tt0) REVERT: O 23 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6621 (mmm160) REVERT: Q 31 ASN cc_start: 0.8812 (m-40) cc_final: 0.8594 (m-40) REVERT: E 121 LYS cc_start: 0.9211 (mtmt) cc_final: 0.8896 (mttm) REVERT: F 577 GLN cc_start: 0.8455 (mt0) cc_final: 0.8223 (mt0) REVERT: F 659 ASP cc_start: 0.8788 (t70) cc_final: 0.8520 (t70) REVERT: P 83 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.6246 (ptp-170) outliers start: 83 outliers final: 27 residues processed: 422 average time/residue: 1.2941 time to fit residues: 636.4141 Evaluate side-chains 376 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 279 optimal weight: 0.0770 chunk 81 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN A 114 GLN A 173 HIS ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN C 428 GLN D 650 GLN D 653 GLN O 3 GLN O 100BGLN Q 69 ASN E 173 HIS E 355 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.175408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140343 restraints weight = 26738.664| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.84 r_work: 0.3326 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25938 Z= 0.123 Angle : 0.590 9.063 35385 Z= 0.290 Chirality : 0.044 0.389 4149 Planarity : 0.004 0.039 4341 Dihedral : 7.779 100.974 5289 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.31 % Allowed : 18.48 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3015 helix: 0.23 (0.26), residues: 432 sheet: 0.19 (0.15), residues: 987 loop : -0.31 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.006 0.001 HIS A 173 PHE 0.012 0.001 PHE A 383 TYR 0.014 0.001 TYR J 91 ARG 0.006 0.000 ARG C 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 45) link_NAG-ASN : angle 2.52110 ( 135) link_ALPHA1-6 : bond 0.02649 ( 3) link_ALPHA1-6 : angle 3.37215 ( 9) link_BETA1-4 : bond 0.00548 ( 42) link_BETA1-4 : angle 1.88324 ( 126) link_ALPHA1-3 : bond 0.00856 ( 6) link_ALPHA1-3 : angle 2.87578 ( 18) hydrogen bonds : bond 0.03646 ( 924) hydrogen bonds : angle 5.22233 ( 2673) SS BOND : bond 0.00241 ( 48) SS BOND : angle 1.33113 ( 96) covalent geometry : bond 0.00270 (25794) covalent geometry : angle 0.55059 (35001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 368 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7394 (mmm160) REVERT: A 121 LYS cc_start: 0.9266 (mtpt) cc_final: 0.8876 (mttt) REVERT: B 574 LYS cc_start: 0.8455 (mmtp) cc_final: 0.8165 (mttm) REVERT: H 54 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8855 (tpt170) REVERT: H 69 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7876 (mtt) REVERT: H 81 GLU cc_start: 0.8094 (tt0) cc_final: 0.7577 (tt0) REVERT: H 108 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7867 (tt) REVERT: L 33 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8181 (tt) REVERT: M 53 GLN cc_start: 0.8615 (mm110) cc_final: 0.8204 (mm110) REVERT: M 95 GLN cc_start: 0.8526 (mp-120) cc_final: 0.8124 (mm110) REVERT: C 61 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4333 (t80) REVERT: C 84 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8610 (mp) REVERT: C 479 TRP cc_start: 0.7622 (m-10) cc_final: 0.7299 (m-10) REVERT: D 577 GLN cc_start: 0.8466 (mt0) cc_final: 0.8201 (mt0) REVERT: D 647 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7121 (tm-30) REVERT: K 46 GLU cc_start: 0.8207 (tt0) cc_final: 0.7905 (tt0) REVERT: K 81 GLU cc_start: 0.8253 (tt0) cc_final: 0.7840 (tt0) REVERT: N 33 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8222 (tt) REVERT: O 23 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6871 (tmt170) REVERT: E 121 LYS cc_start: 0.9203 (mtmt) cc_final: 0.8926 (mttm) REVERT: E 475 MET cc_start: 0.8930 (mmt) cc_final: 0.8193 (mpm) REVERT: F 577 GLN cc_start: 0.8543 (mt0) cc_final: 0.8329 (mt0) REVERT: P 69 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8561 (mpt) outliers start: 61 outliers final: 25 residues processed: 401 average time/residue: 1.3399 time to fit residues: 626.2833 Evaluate side-chains 382 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 347 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 69 MET Chi-restraints excluded: chain P residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 80 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 296 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN A 114 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN J 39 GLN J 105 GLN M 38 GLN C 173 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 69 ASN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN P 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133209 restraints weight = 26681.493| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.77 r_work: 0.3184 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 25938 Z= 0.389 Angle : 0.850 11.872 35385 Z= 0.420 Chirality : 0.054 0.225 4149 Planarity : 0.006 0.048 4341 Dihedral : 8.272 94.204 5289 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.70 % Allowed : 17.46 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3015 helix: -0.22 (0.25), residues: 438 sheet: -0.04 (0.16), residues: 975 loop : -0.57 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP P 50 HIS 0.007 0.002 HIS E 249 PHE 0.020 0.003 PHE G 100H TYR 0.021 0.003 TYR J 91 ARG 0.006 0.001 ARG E 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00917 ( 45) link_NAG-ASN : angle 2.85570 ( 135) link_ALPHA1-6 : bond 0.02508 ( 3) link_ALPHA1-6 : angle 3.55556 ( 9) link_BETA1-4 : bond 0.00624 ( 42) link_BETA1-4 : angle 2.08509 ( 126) link_ALPHA1-3 : bond 0.00700 ( 6) link_ALPHA1-3 : angle 3.19312 ( 18) hydrogen bonds : bond 0.05568 ( 924) hydrogen bonds : angle 5.62209 ( 2673) SS BOND : bond 0.00642 ( 48) SS BOND : angle 2.10351 ( 96) covalent geometry : bond 0.00934 (25794) covalent geometry : angle 0.81405 (35001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 350 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7311 (mmm160) REVERT: I 31 ASN cc_start: 0.8883 (m110) cc_final: 0.8633 (m-40) REVERT: A 103 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: A 121 LYS cc_start: 0.9308 (mtpt) cc_final: 0.8938 (mttt) REVERT: A 129 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9007 (mt) REVERT: A 207 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7334 (mmtm) REVERT: A 231 LYS cc_start: 0.8472 (mttp) cc_final: 0.8168 (mttt) REVERT: A 370 GLU cc_start: 0.8797 (mp0) cc_final: 0.8172 (mp0) REVERT: A 432 GLN cc_start: 0.8218 (mt0) cc_final: 0.7319 (mm-40) REVERT: B 574 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8226 (mttm) REVERT: B 647 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: H 54 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8881 (tpt170) REVERT: H 81 GLU cc_start: 0.8243 (tt0) cc_final: 0.7905 (tt0) REVERT: H 108 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7886 (tt) REVERT: L 39 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7395 (mptt) REVERT: C 61 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4237 (t80) REVERT: C 84 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8878 (mp) REVERT: C 103 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: C 479 TRP cc_start: 0.7653 (m-10) cc_final: 0.6924 (m-10) REVERT: D 574 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8158 (mttm) REVERT: D 577 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: D 584 GLU cc_start: 0.8748 (pt0) cc_final: 0.8530 (pt0) REVERT: K 21 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8334 (m) REVERT: K 46 GLU cc_start: 0.8344 (tt0) cc_final: 0.8090 (tt0) REVERT: K 69 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7798 (mtm) REVERT: K 81 GLU cc_start: 0.8379 (tt0) cc_final: 0.7969 (tt0) REVERT: N 33 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8281 (tt) REVERT: O 23 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6633 (mmm160) REVERT: Q 31 ASN cc_start: 0.8933 (m-40) cc_final: 0.8732 (m-40) REVERT: E 84 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8867 (mp) REVERT: E 121 LYS cc_start: 0.9230 (mtmt) cc_final: 0.8947 (mttm) REVERT: E 315 GLN cc_start: 0.8224 (mt0) cc_final: 0.7781 (mm110) REVERT: E 327 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6973 (mtm180) REVERT: E 475 MET cc_start: 0.8968 (mmt) cc_final: 0.8767 (mpm) REVERT: F 577 GLN cc_start: 0.8512 (mt0) cc_final: 0.8302 (mt0) REVERT: F 647 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: P 83 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6337 (ptt180) REVERT: P 100 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8624 (p0) outliers start: 98 outliers final: 45 residues processed: 407 average time/residue: 1.4502 time to fit residues: 677.5791 Evaluate side-chains 398 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 333 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 1 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 490 LYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 281 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 254 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN A 114 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN O 3 GLN O 100BGLN E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.171333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135386 restraints weight = 26406.464| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.86 r_work: 0.3285 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25938 Z= 0.147 Angle : 0.625 9.275 35385 Z= 0.309 Chirality : 0.044 0.191 4149 Planarity : 0.004 0.044 4341 Dihedral : 7.691 92.689 5289 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.65 % Allowed : 18.93 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3015 helix: 0.18 (0.26), residues: 432 sheet: 0.19 (0.16), residues: 948 loop : -0.44 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 50 HIS 0.003 0.001 HIS P 32 PHE 0.012 0.001 PHE A 383 TYR 0.014 0.001 TYR Q 96 ARG 0.007 0.000 ARG C 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 45) link_NAG-ASN : angle 2.64779 ( 135) link_ALPHA1-6 : bond 0.03061 ( 3) link_ALPHA1-6 : angle 3.73339 ( 9) link_BETA1-4 : bond 0.00527 ( 42) link_BETA1-4 : angle 1.80032 ( 126) link_ALPHA1-3 : bond 0.00840 ( 6) link_ALPHA1-3 : angle 3.20216 ( 18) hydrogen bonds : bond 0.04020 ( 924) hydrogen bonds : angle 5.35452 ( 2673) SS BOND : bond 0.00275 ( 48) SS BOND : angle 1.41049 ( 96) covalent geometry : bond 0.00332 (25794) covalent geometry : angle 0.58518 (35001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7378 (mmm160) REVERT: I 31 ASN cc_start: 0.8648 (m110) cc_final: 0.8310 (m-40) REVERT: A 103 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: A 121 LYS cc_start: 0.9324 (mtpt) cc_final: 0.8900 (mttt) REVERT: A 268 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 315 GLN cc_start: 0.7928 (mt0) cc_final: 0.7456 (mm110) REVERT: B 574 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8226 (mttm) REVERT: H 21 SER cc_start: 0.8739 (p) cc_final: 0.8388 (t) REVERT: H 54 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8853 (tpt170) REVERT: H 108 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 61 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.4305 (t80) REVERT: C 84 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 479 TRP cc_start: 0.7636 (m-10) cc_final: 0.7052 (m-10) REVERT: D 577 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: K 46 GLU cc_start: 0.8259 (tt0) cc_final: 0.7971 (tt0) REVERT: N 33 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8229 (tt) REVERT: O 23 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6876 (tmt170) REVERT: Q 31 ASN cc_start: 0.8816 (m-40) cc_final: 0.8570 (m-40) REVERT: E 84 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8635 (mp) REVERT: E 121 LYS cc_start: 0.9251 (mtmt) cc_final: 0.8949 (mttm) REVERT: E 315 GLN cc_start: 0.8025 (mt0) cc_final: 0.7576 (mm110) REVERT: E 322 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: E 327 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6786 (mtm180) REVERT: E 475 MET cc_start: 0.8966 (mmt) cc_final: 0.8605 (mpm) REVERT: F 577 GLN cc_start: 0.8436 (mt0) cc_final: 0.8216 (mt0) REVERT: P 83 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6283 (ptt180) REVERT: P 100 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8483 (p0) outliers start: 70 outliers final: 30 residues processed: 397 average time/residue: 1.3316 time to fit residues: 621.8706 Evaluate side-chains 381 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 chunk 191 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN A 114 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 69 ASN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137198 restraints weight = 26706.977| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.84 r_work: 0.3270 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25938 Z= 0.151 Angle : 0.617 8.867 35385 Z= 0.304 Chirality : 0.044 0.165 4149 Planarity : 0.004 0.043 4341 Dihedral : 7.521 90.552 5289 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 18.97 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3015 helix: 0.32 (0.26), residues: 432 sheet: 0.26 (0.16), residues: 948 loop : -0.39 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 50 HIS 0.003 0.001 HIS P 32 PHE 0.012 0.001 PHE A 383 TYR 0.017 0.001 TYR J 91 ARG 0.007 0.000 ARG C 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 45) link_NAG-ASN : angle 2.57851 ( 135) link_ALPHA1-6 : bond 0.02881 ( 3) link_ALPHA1-6 : angle 3.66709 ( 9) link_BETA1-4 : bond 0.00511 ( 42) link_BETA1-4 : angle 1.68685 ( 126) link_ALPHA1-3 : bond 0.00851 ( 6) link_ALPHA1-3 : angle 3.23578 ( 18) hydrogen bonds : bond 0.03916 ( 924) hydrogen bonds : angle 5.24271 ( 2673) SS BOND : bond 0.00273 ( 48) SS BOND : angle 1.32352 ( 96) covalent geometry : bond 0.00344 (25794) covalent geometry : angle 0.57894 (35001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7285 (mmm160) REVERT: I 31 ASN cc_start: 0.8745 (m110) cc_final: 0.8416 (m-40) REVERT: A 121 LYS cc_start: 0.9331 (mtpt) cc_final: 0.8896 (mttt) REVERT: A 315 GLN cc_start: 0.7966 (mt0) cc_final: 0.7452 (mm110) REVERT: A 479 TRP cc_start: 0.7683 (m-10) cc_final: 0.7273 (m-10) REVERT: B 574 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8220 (mttm) REVERT: H 21 SER cc_start: 0.8688 (p) cc_final: 0.8353 (t) REVERT: H 54 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8856 (tpt170) REVERT: H 108 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7933 (tt) REVERT: L 39 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7321 (mptt) REVERT: M 95 GLN cc_start: 0.8593 (mp-120) cc_final: 0.8196 (mm110) REVERT: C 61 TYR cc_start: 0.5159 (OUTLIER) cc_final: 0.4298 (t80) REVERT: C 84 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 479 TRP cc_start: 0.7640 (m-10) cc_final: 0.7083 (m-10) REVERT: D 577 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: K 46 GLU cc_start: 0.8260 (tt0) cc_final: 0.7980 (tt0) REVERT: N 33 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8208 (tt) REVERT: O 23 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6618 (mmm160) REVERT: Q 31 ASN cc_start: 0.8874 (m-40) cc_final: 0.8638 (m-40) REVERT: E 84 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8654 (mp) REVERT: E 121 LYS cc_start: 0.9238 (mtmt) cc_final: 0.8935 (mttm) REVERT: E 315 GLN cc_start: 0.8063 (mt0) cc_final: 0.7635 (mm110) REVERT: E 327 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6778 (mtm180) REVERT: E 475 MET cc_start: 0.8973 (mmt) cc_final: 0.8575 (mpm) REVERT: F 536 THR cc_start: 0.8951 (p) cc_final: 0.8636 (p) REVERT: F 577 GLN cc_start: 0.8468 (mt0) cc_final: 0.8248 (mt0) REVERT: P 83 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6261 (ptt180) REVERT: P 100 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8522 (p0) REVERT: R 33 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8162 (tt) outliers start: 67 outliers final: 32 residues processed: 398 average time/residue: 1.3199 time to fit residues: 610.3884 Evaluate side-chains 389 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 343 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 266 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 254 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN O 3 GLN O 100BGLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.170250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135916 restraints weight = 26723.592| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.83 r_work: 0.3236 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 25938 Z= 0.235 Angle : 0.693 9.099 35385 Z= 0.341 Chirality : 0.047 0.239 4149 Planarity : 0.004 0.034 4341 Dihedral : 7.609 86.403 5289 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 2.65 % Allowed : 19.12 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3015 helix: 0.17 (0.26), residues: 438 sheet: 0.20 (0.16), residues: 957 loop : -0.49 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 50 HIS 0.004 0.001 HIS E 249 PHE 0.017 0.002 PHE C 353 TYR 0.018 0.002 TYR J 91 ARG 0.007 0.001 ARG C 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 45) link_NAG-ASN : angle 2.68623 ( 135) link_ALPHA1-6 : bond 0.02778 ( 3) link_ALPHA1-6 : angle 3.65948 ( 9) link_BETA1-4 : bond 0.00526 ( 42) link_BETA1-4 : angle 1.71327 ( 126) link_ALPHA1-3 : bond 0.00829 ( 6) link_ALPHA1-3 : angle 3.36982 ( 18) hydrogen bonds : bond 0.04512 ( 924) hydrogen bonds : angle 5.32294 ( 2673) SS BOND : bond 0.00405 ( 48) SS BOND : angle 1.56323 ( 96) covalent geometry : bond 0.00553 (25794) covalent geometry : angle 0.65617 (35001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 348 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7382 (mmm160) REVERT: I 31 ASN cc_start: 0.8851 (m110) cc_final: 0.8572 (m-40) REVERT: A 121 LYS cc_start: 0.9368 (mtpt) cc_final: 0.8956 (mttt) REVERT: A 207 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7390 (mmmm) REVERT: A 315 GLN cc_start: 0.8077 (mt0) cc_final: 0.7576 (mm110) REVERT: A 432 GLN cc_start: 0.8207 (mt0) cc_final: 0.7329 (mm-40) REVERT: A 464 THR cc_start: 0.9133 (p) cc_final: 0.8854 (p) REVERT: A 479 TRP cc_start: 0.7741 (m-10) cc_final: 0.7293 (m-10) REVERT: B 574 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8283 (mttm) REVERT: B 647 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: H 21 SER cc_start: 0.8699 (p) cc_final: 0.8387 (t) REVERT: H 54 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8887 (tpt170) REVERT: L 33 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8198 (tt) REVERT: L 39 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7371 (mptt) REVERT: C 61 TYR cc_start: 0.5138 (OUTLIER) cc_final: 0.4247 (t80) REVERT: C 84 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8786 (mp) REVERT: C 129 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9044 (mt) REVERT: C 207 LYS cc_start: 0.7937 (mmpt) cc_final: 0.7529 (mmtm) REVERT: C 479 TRP cc_start: 0.7746 (m-10) cc_final: 0.7077 (m-10) REVERT: D 574 LYS cc_start: 0.8399 (mmtp) cc_final: 0.8140 (mttm) REVERT: D 577 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: K 21 SER cc_start: 0.8685 (p) cc_final: 0.8370 (m) REVERT: K 46 GLU cc_start: 0.8331 (tt0) cc_final: 0.8049 (tt0) REVERT: K 48 MET cc_start: 0.9061 (mtp) cc_final: 0.8829 (mtp) REVERT: K 69 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7698 (mtm) REVERT: N 33 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8282 (tt) REVERT: O 23 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6649 (mmm160) REVERT: Q 31 ASN cc_start: 0.8964 (m-40) cc_final: 0.8742 (m-40) REVERT: E 84 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8743 (mp) REVERT: E 121 LYS cc_start: 0.9279 (mtmt) cc_final: 0.9006 (mttm) REVERT: E 315 GLN cc_start: 0.8135 (mt0) cc_final: 0.7729 (mm110) REVERT: E 327 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6854 (mtm180) REVERT: E 475 MET cc_start: 0.8973 (mmt) cc_final: 0.8645 (mpm) REVERT: F 577 GLN cc_start: 0.8490 (mt0) cc_final: 0.8270 (mt0) REVERT: P 83 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6337 (ptt180) REVERT: R 33 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8137 (tt) outliers start: 70 outliers final: 37 residues processed: 394 average time/residue: 1.3174 time to fit residues: 601.0475 Evaluate side-chains 392 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 143 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 280 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN A 114 GLN A 216 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137241 restraints weight = 26838.768| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.83 r_work: 0.3272 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25938 Z= 0.142 Angle : 0.611 8.857 35385 Z= 0.301 Chirality : 0.043 0.192 4149 Planarity : 0.004 0.032 4341 Dihedral : 7.328 83.944 5289 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 2.23 % Allowed : 19.73 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3015 helix: 0.37 (0.26), residues: 432 sheet: 0.29 (0.16), residues: 951 loop : -0.40 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 50 HIS 0.003 0.001 HIS P 32 PHE 0.012 0.001 PHE A 383 TYR 0.016 0.001 TYR J 91 ARG 0.008 0.000 ARG E 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 45) link_NAG-ASN : angle 2.50398 ( 135) link_ALPHA1-6 : bond 0.02890 ( 3) link_ALPHA1-6 : angle 3.66284 ( 9) link_BETA1-4 : bond 0.00493 ( 42) link_BETA1-4 : angle 1.63950 ( 126) link_ALPHA1-3 : bond 0.00866 ( 6) link_ALPHA1-3 : angle 3.38284 ( 18) hydrogen bonds : bond 0.03852 ( 924) hydrogen bonds : angle 5.19448 ( 2673) SS BOND : bond 0.00269 ( 48) SS BOND : angle 1.25594 ( 96) covalent geometry : bond 0.00323 (25794) covalent geometry : angle 0.57438 (35001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 349 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7233 (mmm160) REVERT: G 81 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8277 (tp-100) REVERT: I 31 ASN cc_start: 0.8678 (m110) cc_final: 0.8327 (m-40) REVERT: A 121 LYS cc_start: 0.9324 (mtpt) cc_final: 0.8899 (mttt) REVERT: A 315 GLN cc_start: 0.7961 (mt0) cc_final: 0.7439 (mm110) REVERT: A 432 GLN cc_start: 0.8094 (mt0) cc_final: 0.7857 (mt0) REVERT: A 479 TRP cc_start: 0.7681 (m-10) cc_final: 0.7281 (m-10) REVERT: B 574 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8187 (mttm) REVERT: H 21 SER cc_start: 0.8648 (p) cc_final: 0.8321 (t) REVERT: H 54 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8856 (tpt170) REVERT: L 39 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7291 (mptt) REVERT: C 61 TYR cc_start: 0.5089 (OUTLIER) cc_final: 0.4202 (t80) REVERT: C 84 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8613 (mp) REVERT: C 479 TRP cc_start: 0.7629 (m-10) cc_final: 0.7078 (m-10) REVERT: D 577 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: K 21 SER cc_start: 0.8633 (p) cc_final: 0.8327 (m) REVERT: K 46 GLU cc_start: 0.8268 (tt0) cc_final: 0.7995 (tt0) REVERT: N 33 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8206 (tt) REVERT: O 23 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6632 (mmm160) REVERT: Q 31 ASN cc_start: 0.8846 (m-40) cc_final: 0.8608 (m-40) REVERT: E 84 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8637 (mp) REVERT: E 121 LYS cc_start: 0.9235 (mtmt) cc_final: 0.8945 (mttm) REVERT: E 315 GLN cc_start: 0.8037 (mt0) cc_final: 0.7614 (mm110) REVERT: E 475 MET cc_start: 0.8951 (mmt) cc_final: 0.8617 (mpm) REVERT: F 536 THR cc_start: 0.8960 (p) cc_final: 0.8647 (p) REVERT: F 577 GLN cc_start: 0.8438 (mt0) cc_final: 0.8222 (mt0) REVERT: P 83 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.6227 (ptt180) REVERT: R 33 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8140 (tt) outliers start: 59 outliers final: 34 residues processed: 387 average time/residue: 1.5129 time to fit residues: 689.3441 Evaluate side-chains 386 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 341 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 220 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 246 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 130 optimal weight: 0.0270 chunk 177 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 114 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 69 ASN Q 95 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137722 restraints weight = 26699.070| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.87 r_work: 0.3287 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25938 Z= 0.130 Angle : 0.596 8.842 35385 Z= 0.294 Chirality : 0.043 0.181 4149 Planarity : 0.004 0.033 4341 Dihedral : 7.166 81.532 5289 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Rotamer: Outliers : 1.85 % Allowed : 20.03 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3015 helix: 0.49 (0.27), residues: 432 sheet: 0.35 (0.16), residues: 951 loop : -0.38 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 50 HIS 0.003 0.001 HIS P 32 PHE 0.012 0.001 PHE A 383 TYR 0.016 0.001 TYR J 91 ARG 0.008 0.000 ARG E 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 45) link_NAG-ASN : angle 2.40584 ( 135) link_ALPHA1-6 : bond 0.02889 ( 3) link_ALPHA1-6 : angle 3.68722 ( 9) link_BETA1-4 : bond 0.00489 ( 42) link_BETA1-4 : angle 1.58115 ( 126) link_ALPHA1-3 : bond 0.00879 ( 6) link_ALPHA1-3 : angle 3.41357 ( 18) hydrogen bonds : bond 0.03678 ( 924) hydrogen bonds : angle 5.10301 ( 2673) SS BOND : bond 0.00246 ( 48) SS BOND : angle 1.19061 ( 96) covalent geometry : bond 0.00292 (25794) covalent geometry : angle 0.56112 (35001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 347 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7279 (mmm160) REVERT: I 31 ASN cc_start: 0.8703 (m110) cc_final: 0.8391 (m-40) REVERT: A 121 LYS cc_start: 0.9303 (mtpt) cc_final: 0.8885 (mttt) REVERT: A 315 GLN cc_start: 0.7989 (mt0) cc_final: 0.7427 (mm110) REVERT: A 432 GLN cc_start: 0.8081 (mt0) cc_final: 0.7861 (mt0) REVERT: A 479 TRP cc_start: 0.7624 (m-10) cc_final: 0.7180 (m-10) REVERT: B 574 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8158 (mttm) REVERT: H 21 SER cc_start: 0.8642 (p) cc_final: 0.8328 (t) REVERT: H 54 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8866 (tpt170) REVERT: M 47 MET cc_start: 0.8392 (mmm) cc_final: 0.8167 (mmm) REVERT: C 61 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.4208 (t80) REVERT: C 84 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8580 (mp) REVERT: C 479 TRP cc_start: 0.7582 (m-10) cc_final: 0.7105 (m-10) REVERT: D 577 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: K 21 SER cc_start: 0.8659 (p) cc_final: 0.8339 (m) REVERT: K 46 GLU cc_start: 0.8243 (tt0) cc_final: 0.7948 (tt0) REVERT: O 23 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6662 (mmm160) REVERT: Q 31 ASN cc_start: 0.8843 (m-40) cc_final: 0.8603 (m-40) REVERT: E 84 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8604 (mp) REVERT: E 121 LYS cc_start: 0.9222 (mtmt) cc_final: 0.8931 (mttm) REVERT: E 315 GLN cc_start: 0.8023 (mt0) cc_final: 0.7596 (mm110) REVERT: E 475 MET cc_start: 0.8970 (mmt) cc_final: 0.8516 (mpm) REVERT: F 536 THR cc_start: 0.8956 (p) cc_final: 0.8648 (p) REVERT: F 577 GLN cc_start: 0.8440 (mt0) cc_final: 0.8225 (mt0) REVERT: P 83 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6183 (ptt180) REVERT: R 33 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8124 (tt) outliers start: 49 outliers final: 32 residues processed: 375 average time/residue: 1.5008 time to fit residues: 654.5211 Evaluate side-chains 383 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 215 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 125 optimal weight: 0.0270 chunk 200 optimal weight: 7.9990 chunk 252 optimal weight: 0.2980 chunk 138 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 114 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 95 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.173477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137588 restraints weight = 26647.008| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.89 r_work: 0.3298 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 25938 Z= 0.130 Angle : 0.602 12.502 35385 Z= 0.297 Chirality : 0.043 0.192 4149 Planarity : 0.004 0.033 4341 Dihedral : 7.079 79.080 5289 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 20.14 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3015 helix: 0.54 (0.27), residues: 432 sheet: 0.39 (0.16), residues: 951 loop : -0.36 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 50 HIS 0.003 0.001 HIS P 32 PHE 0.012 0.001 PHE A 383 TYR 0.016 0.001 TYR J 91 ARG 0.008 0.000 ARG E 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 45) link_NAG-ASN : angle 2.38985 ( 135) link_ALPHA1-6 : bond 0.02880 ( 3) link_ALPHA1-6 : angle 3.68743 ( 9) link_BETA1-4 : bond 0.00484 ( 42) link_BETA1-4 : angle 1.54046 ( 126) link_ALPHA1-3 : bond 0.00899 ( 6) link_ALPHA1-3 : angle 3.44584 ( 18) hydrogen bonds : bond 0.03611 ( 924) hydrogen bonds : angle 5.06383 ( 2673) SS BOND : bond 0.00245 ( 48) SS BOND : angle 1.65835 ( 96) covalent geometry : bond 0.00296 (25794) covalent geometry : angle 0.56495 (35001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20537.08 seconds wall clock time: 356 minutes 55.62 seconds (21415.62 seconds total)