Starting phenix.real_space_refine on Sun May 25 11:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6u_29783/05_2025/8g6u_29783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6u_29783/05_2025/8g6u_29783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6u_29783/05_2025/8g6u_29783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6u_29783/05_2025/8g6u_29783.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6u_29783/05_2025/8g6u_29783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6u_29783/05_2025/8g6u_29783.cif" } resolution = 3.16 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= -0.014 sd= 0.602 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 138 5.16 5 C 16788 2.51 5 N 4377 2.21 5 O 5568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "O" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "J" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "T" 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: "U" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "b" 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "k" 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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: "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: 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: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" 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: "1" 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: "2" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 17.14, per 1000 atoms: 0.64 Number of scatterers: 26871 At special positions: 0 Unit cell: (169.32, 156.04, 147.74, 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 138 16.00 O 5568 8.00 N 4377 7.00 C 16788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN S 10 " - " MAN S 11 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN U 8 " - " MAN U 9 " " MAN Y 4 " - " MAN Y 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN a 10 " - " MAN a 11 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " " MAN d 5 " - " MAN d 6 " " MAN d 8 " - " MAN d 9 " " MAN h 4 " - " MAN h 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN j 8 " - " MAN j 9 " " MAN j 10 " - " MAN j 11 " " MAN k 4 " - " MAN k 5 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 8 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 10 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " MAN d 7 " - " MAN d 10 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 10 " " BMA T 3 " - " MAN T 6 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 8 " " BMA Y 3 " - " MAN Y 6 " " BMA Z 3 " - " MAN Z 5 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 7 " " MAN d 7 " - " MAN d 8 " " BMA h 3 " - " MAN h 6 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 10 " " BMA k 3 " - " MAN k 6 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA r 3 " - " MAN r 6 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG 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 q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN A 448 " " NAG 1 1 " - " ASN E 448 " " NAG 2 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 187 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 411 " " NAG A 608 " - " ASN A 465 " " NAG A 609 " - " ASN A 392 " " NAG B 700 " - " ASN B 611 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 187 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 355 " " NAG E 607 " - " ASN E 411 " " NAG E 608 " - " ASN E 465 " " NAG E 609 " - " ASN E 392 " " NAG F 700 " - " ASN F 611 " " NAG F 701 " - " ASN F 616 " " NAG F 702 " - " ASN F 625 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 603 " - " ASN I 187 " " NAG I 604 " - " ASN I 295 " " NAG I 605 " - " ASN I 301 " " NAG I 606 " - " ASN I 355 " " NAG I 607 " - " ASN I 411 " " NAG I 608 " - " ASN I 465 " " NAG I 609 " - " ASN I 392 " " NAG J 700 " - " ASN J 611 " " NAG J 701 " - " ASN J 616 " " NAG J 702 " - " ASN J 625 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN E 234 " " NAG b 1 " - " ASN E 276 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN A 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN F 637 " " NAG j 1 " - " ASN I 234 " " NAG k 1 " - " ASN I 276 " " NAG l 1 " - " ASN I 156 " " NAG m 1 " - " ASN I 289 " " NAG n 1 " - " ASN I 332 " " NAG o 1 " - " ASN I 386 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " " NAG t 1 " - " ASN A 130 " " NAG u 1 " - " ASN E 130 " " NAG v 1 " - " ASN A 289 " " NAG w 1 " - " ASN E 289 " " NAG x 1 " - " ASN A 241 " " NAG y 1 " - " ASN E 241 " " NAG z 1 " - " ASN I 241 " Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 3.7 seconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5718 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 57 sheets defined 15.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.640A pdb=" N MET A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.937A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 537 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.796A pdb=" N ILE B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.902A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100D through 100H Processing helix chain 'N' and resid 79 through 84 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU E 351 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.641A pdb=" N MET E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.936A pdb=" N ASN E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 537 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.795A pdb=" N ILE F 622 " --> pdb=" O THR F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.902A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100D through 100H Processing helix chain 'P' and resid 79 through 84 Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU I 351 " --> pdb=" O ASN I 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.640A pdb=" N MET I 373 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.936A pdb=" N ASN I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 537 Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 removed outlier: 3.796A pdb=" N ILE J 622 " --> pdb=" O THR J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 661 Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.903A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.666A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'Q' and resid 100D through 100H Processing helix chain 'R' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.093A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.545A pdb=" N ILE A 271 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS A 331 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.862A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 35 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TYR C 33 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.722A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.617A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.578A pdb=" N GLN M 5 " --> pdb=" O SER M 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA M 93 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR M 35 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG M 100 " --> pdb=" O PHE M 100K" (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE M 100K" --> pdb=" O ARG M 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.559A pdb=" N HIS N 89 " --> pdb=" O GLN N 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.092A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 155 through 162 Processing sheet with id=AC6, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.544A pdb=" N ILE E 271 " --> pdb=" O HIS E 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS E 331 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD1, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.863A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN G 50 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL G 35 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP G 52 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N TYR G 33 " --> pdb=" O TRP G 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.721A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.617A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR H 72 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.579A pdb=" N GLN O 5 " --> pdb=" O SER O 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR O 90 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR O 35 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR O 90 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG O 100 " --> pdb=" O PHE O 100K" (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE O 100K" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.559A pdb=" N HIS P 89 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR P 36 " --> pdb=" O TYR P 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 494 through 499 Processing sheet with id=AE4, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.092A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 92 through 94 Processing sheet with id=AE6, first strand: chain 'I' and resid 155 through 162 Processing sheet with id=AE7, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE8, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.544A pdb=" N ILE I 271 " --> pdb=" O HIS I 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS I 331 " --> pdb=" O ILE I 416 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS I 296 " --> pdb=" O CYS I 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AF2, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AF3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.863A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N TYR K 33 " --> pdb=" O TRP K 52 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.722A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.616A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.577A pdb=" N GLN Q 5 " --> pdb=" O SER Q 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.254A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR Q 90 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA Q 93 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR Q 35 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.254A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR Q 90 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG Q 100 " --> pdb=" O PHE Q 100K" (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE Q 100K" --> pdb=" O ARG Q 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.560A pdb=" N HIS R 89 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR R 36 " --> pdb=" O TYR R 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.77 Time building geometry restraints manager: 10.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7692 1.34 - 1.46: 5853 1.46 - 1.58: 13698 1.58 - 1.70: 6 1.70 - 1.82: 186 Bond restraints: 27435 Sorted by residual: bond pdb=" N LEU F 544 " pdb=" CA LEU F 544 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" N LEU B 544 " pdb=" CA LEU B 544 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" N LEU J 544 " pdb=" CA LEU J 544 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.45e+01 bond pdb=" C1 NAG E 603 " pdb=" O5 NAG E 603 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG I 603 " pdb=" O5 NAG I 603 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 27430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 36195 2.62 - 5.24: 849 5.24 - 7.86: 177 7.86 - 10.48: 30 10.48 - 13.10: 12 Bond angle restraints: 37263 Sorted by residual: angle pdb=" C PRO O 41 " pdb=" CA PRO O 41 " pdb=" CB PRO O 41 " ideal model delta sigma weight residual 111.56 124.66 -13.10 1.65e+00 3.67e-01 6.30e+01 angle pdb=" C PRO Q 41 " pdb=" CA PRO Q 41 " pdb=" CB PRO Q 41 " ideal model delta sigma weight residual 111.56 124.65 -13.09 1.65e+00 3.67e-01 6.29e+01 angle pdb=" C PRO M 41 " pdb=" CA PRO M 41 " pdb=" CB PRO M 41 " ideal model delta sigma weight residual 111.56 124.64 -13.08 1.65e+00 3.67e-01 6.28e+01 angle pdb=" N ARG F 542 " pdb=" CA ARG F 542 " pdb=" C ARG F 542 " ideal model delta sigma weight residual 107.49 119.28 -11.79 1.74e+00 3.30e-01 4.59e+01 angle pdb=" N ARG B 542 " pdb=" CA ARG B 542 " pdb=" C ARG B 542 " ideal model delta sigma weight residual 107.49 119.27 -11.78 1.74e+00 3.30e-01 4.58e+01 ... (remaining 37258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.58: 17235 24.58 - 49.15: 980 49.15 - 73.73: 248 73.73 - 98.31: 140 98.31 - 122.88: 108 Dihedral angle restraints: 18711 sinusoidal: 9786 harmonic: 8925 Sorted by residual: dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.23 -82.77 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.28 -82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.28 -82.72 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 18708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4641 0.168 - 0.337: 45 0.337 - 0.505: 6 0.505 - 0.674: 3 0.674 - 0.842: 12 Chirality restraints: 4707 Sorted by residual: chirality pdb=" C1 NAG 2 1 " pdb=" ND2 ASN I 448 " pdb=" C2 NAG 2 1 " pdb=" O5 NAG 2 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" C1 NAG 1 1 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG 1 1 " pdb=" O5 NAG 1 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4704 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 386 " 0.011 2.00e-02 2.50e+03 6.99e-02 6.10e+01 pdb=" CG ASN A 386 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 386 " 0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN A 386 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 386 " -0.011 2.00e-02 2.50e+03 6.96e-02 6.05e+01 pdb=" CG ASN E 386 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN E 386 " -0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN E 386 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 386 " -0.011 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" CG ASN I 386 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN I 386 " -0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN I 386 " 0.084 2.00e-02 2.50e+03 pdb=" C1 NAG o 1 " -0.069 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 278 2.54 - 3.13: 20837 3.13 - 3.72: 38379 3.72 - 4.31: 55133 4.31 - 4.90: 92275 Nonbonded interactions: 206902 Sorted by model distance: nonbonded pdb=" O GLN F 543 " pdb=" O LEU F 544 " model vdw 1.945 3.040 nonbonded pdb=" O GLN B 543 " pdb=" O LEU B 544 " model vdw 1.945 3.040 nonbonded pdb=" O GLN J 543 " pdb=" O LEU J 544 " model vdw 1.946 3.040 nonbonded pdb=" N GLU B 620 " pdb=" OE1 GLU B 620 " model vdw 2.056 3.120 nonbonded pdb=" N GLU J 620 " pdb=" OE1 GLU J 620 " model vdw 2.056 3.120 ... (remaining 206897 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 2 or resid 5 through 11)) selection = (chain 'U' and (resid 1 or resid 4 through 10)) selection = (chain 'a' and (resid 2 or resid 5 through 11)) selection = (chain 'd' and (resid 1 or resid 4 through 10)) selection = (chain 'j' and (resid 2 or resid 5 through 11)) selection = (chain 'n' and (resid 1 or resid 4 through 10)) } ncs_group { reference = chain 'T' selection = chain 'Y' selection = chain 'b' selection = chain 'h' selection = chain 'k' selection = chain 'r' } ncs_group { reference = chain 'Z' 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: 17.440 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.200 Process input model: 60.150 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27672 Z= 0.295 Angle : 1.129 23.078 37929 Z= 0.527 Chirality : 0.070 0.842 4707 Planarity : 0.007 0.097 4446 Dihedral : 19.478 122.885 12858 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.56 % Favored : 91.45 % Rotamer: Outliers : 3.79 % Allowed : 1.93 % Favored : 94.28 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 3054 helix: 1.65 (0.27), residues: 381 sheet: -0.19 (0.19), residues: 795 loop : -2.04 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 69 HIS 0.003 0.001 HIS I 287 PHE 0.013 0.001 PHE E 288 TYR 0.019 0.001 TYR R 49 ARG 0.007 0.001 ARG H 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00879 ( 72) link_NAG-ASN : angle 6.80255 ( 216) link_ALPHA1-6 : bond 0.00367 ( 21) link_ALPHA1-6 : angle 1.85561 ( 63) link_BETA1-4 : bond 0.00711 ( 51) link_BETA1-4 : angle 2.16681 ( 153) link_ALPHA1-2 : bond 0.00476 ( 27) link_ALPHA1-2 : angle 1.59671 ( 81) link_ALPHA1-3 : bond 0.00352 ( 21) link_ALPHA1-3 : angle 1.98881 ( 63) hydrogen bonds : bond 0.22036 ( 708) hydrogen bonds : angle 8.41360 ( 1836) SS BOND : bond 0.00470 ( 45) SS BOND : angle 1.54818 ( 90) covalent geometry : bond 0.00567 (27435) covalent geometry : angle 0.99315 (37263) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 612 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 545 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4601 (tp) REVERT: C 66 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8032 (ttt-90) REVERT: G 13 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8380 (mmmt) REVERT: H 4 MET cc_start: 0.7499 (ttm) cc_final: 0.7054 (ttm) REVERT: H 88 CYS cc_start: 0.5394 (p) cc_final: 0.5050 (p) REVERT: O 100 MET cc_start: 0.8126 (mpp) cc_final: 0.7355 (mpp) REVERT: I 103 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7711 (tp40) REVERT: I 107 ASP cc_start: 0.8100 (m-30) cc_final: 0.7884 (m-30) REVERT: L 24 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7642 (ttm110) REVERT: Q 100 TYR cc_start: 0.7833 (m-10) cc_final: 0.7221 (m-10) outliers start: 102 outliers final: 31 residues processed: 662 average time/residue: 0.3607 time to fit residues: 380.8013 Evaluate side-chains 511 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 476 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 503 ARG Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 650 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain P residue 95 SER Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 650 GLN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain R residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 0.0270 chunk 239 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 229 ASN B 540 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN B 653 GLN C 50 GLN D 6 GLN M 64 ASN E 229 ASN F 540 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 GLN O 64 ASN I 103 GLN I 229 ASN J 540 GLN J 641 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.157440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112489 restraints weight = 41930.628| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.23 r_work: 0.3285 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 27672 Z= 0.312 Angle : 1.039 22.720 37929 Z= 0.474 Chirality : 0.061 0.620 4707 Planarity : 0.007 0.145 4446 Dihedral : 16.238 107.902 7309 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.35 % Favored : 90.70 % Rotamer: Outliers : 4.24 % Allowed : 12.15 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 3054 helix: 0.90 (0.26), residues: 420 sheet: -0.56 (0.17), residues: 918 loop : -1.94 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 91 HIS 0.006 0.002 HIS A 287 PHE 0.023 0.003 PHE A 383 TYR 0.021 0.002 TYR A 384 ARG 0.015 0.001 ARG A 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 72) link_NAG-ASN : angle 5.73254 ( 216) link_ALPHA1-6 : bond 0.00559 ( 21) link_ALPHA1-6 : angle 1.84247 ( 63) link_BETA1-4 : bond 0.00673 ( 51) link_BETA1-4 : angle 2.96609 ( 153) link_ALPHA1-2 : bond 0.00992 ( 27) link_ALPHA1-2 : angle 2.26437 ( 81) link_ALPHA1-3 : bond 0.00954 ( 21) link_ALPHA1-3 : angle 2.48952 ( 63) hydrogen bonds : bond 0.05298 ( 708) hydrogen bonds : angle 6.35094 ( 1836) SS BOND : bond 0.01148 ( 45) SS BOND : angle 1.75999 ( 90) covalent geometry : bond 0.00730 (27435) covalent geometry : angle 0.91465 (37263) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 511 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.8427 (mmt) cc_final: 0.8141 (mmt) REVERT: B 530 MET cc_start: 0.7367 (mmm) cc_final: 0.6920 (mtt) REVERT: C 100 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7733 (ttt180) REVERT: D 23 CYS cc_start: 0.7635 (p) cc_final: 0.7383 (p) REVERT: D 24 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8003 (ttm110) REVERT: M 100 TYR cc_start: 0.8498 (p90) cc_final: 0.8262 (p90) REVERT: N 35 TRP cc_start: 0.7516 (m100) cc_final: 0.6694 (m100) REVERT: N 49 TYR cc_start: 0.7924 (p90) cc_final: 0.7585 (p90) REVERT: E 99 ASN cc_start: 0.8952 (t0) cc_final: 0.8610 (t0) REVERT: E 103 GLN cc_start: 0.8756 (tp40) cc_final: 0.8548 (mm-40) REVERT: E 368 ASP cc_start: 0.7539 (m-30) cc_final: 0.7277 (m-30) REVERT: F 652 GLN cc_start: 0.8062 (tp40) cc_final: 0.7832 (tp40) REVERT: G 86 ASP cc_start: 0.9071 (m-30) cc_final: 0.8832 (m-30) REVERT: P 35 TRP cc_start: 0.7358 (m100) cc_final: 0.6992 (m100) REVERT: P 50 ASN cc_start: 0.7346 (t0) cc_final: 0.7140 (t0) REVERT: I 99 ASN cc_start: 0.8883 (t0) cc_final: 0.8590 (t0) REVERT: I 103 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8116 (mm-40) REVERT: I 104 MET cc_start: 0.9113 (ttt) cc_final: 0.8807 (ttt) REVERT: I 107 ASP cc_start: 0.8716 (m-30) cc_final: 0.8481 (m-30) REVERT: J 530 MET cc_start: 0.7361 (mmm) cc_final: 0.7133 (mtt) REVERT: K 66 ARG cc_start: 0.8776 (mtp85) cc_final: 0.8369 (ttt90) REVERT: L 20 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8316 (tpp-160) REVERT: L 24 ARG cc_start: 0.8454 (ttm110) cc_final: 0.8238 (ttm110) REVERT: Q 74 SER cc_start: 0.7649 (p) cc_final: 0.7293 (m) REVERT: R 97 SER cc_start: 0.9367 (t) cc_final: 0.9127 (t) outliers start: 114 outliers final: 72 residues processed: 596 average time/residue: 0.3436 time to fit residues: 330.3902 Evaluate side-chains 537 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 464 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 41 PRO Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 20 ARG Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 266 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 176 optimal weight: 0.2980 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 295 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN B 653 GLN M 99 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 GLN K 43 GLN R 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.163500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118974 restraints weight = 41900.750| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.26 r_work: 0.3377 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27672 Z= 0.145 Angle : 0.811 15.425 37929 Z= 0.368 Chirality : 0.051 0.454 4707 Planarity : 0.006 0.149 4446 Dihedral : 14.670 100.858 7240 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.56 % Favored : 91.85 % Rotamer: Outliers : 3.38 % Allowed : 17.06 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3054 helix: 1.43 (0.26), residues: 417 sheet: -0.69 (0.17), residues: 954 loop : -1.88 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.003 0.001 HIS A 249 PHE 0.011 0.001 PHE F 592 TYR 0.019 0.001 TYR C 47 ARG 0.005 0.000 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 72) link_NAG-ASN : angle 4.39819 ( 216) link_ALPHA1-6 : bond 0.00648 ( 21) link_ALPHA1-6 : angle 1.83305 ( 63) link_BETA1-4 : bond 0.00540 ( 51) link_BETA1-4 : angle 1.96402 ( 153) link_ALPHA1-2 : bond 0.00957 ( 27) link_ALPHA1-2 : angle 1.71507 ( 81) link_ALPHA1-3 : bond 0.01081 ( 21) link_ALPHA1-3 : angle 2.06766 ( 63) hydrogen bonds : bond 0.04597 ( 708) hydrogen bonds : angle 5.77313 ( 1836) SS BOND : bond 0.00729 ( 45) SS BOND : angle 1.45036 ( 90) covalent geometry : bond 0.00313 (27435) covalent geometry : angle 0.71885 (37263) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 518 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8784 (m-30) cc_final: 0.8301 (m-30) REVERT: A 368 ASP cc_start: 0.7512 (m-30) cc_final: 0.7219 (m-30) REVERT: B 545 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4703 (tp) REVERT: C 100 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7619 (ttt180) REVERT: D 24 ARG cc_start: 0.8550 (ttm110) cc_final: 0.7856 (ttm110) REVERT: M 97 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8048 (ttp80) REVERT: N 35 TRP cc_start: 0.7448 (m100) cc_final: 0.6916 (m100) REVERT: N 47 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8297 (mm) REVERT: N 49 TYR cc_start: 0.7935 (p90) cc_final: 0.7639 (p90) REVERT: E 99 ASN cc_start: 0.8936 (t0) cc_final: 0.8580 (t0) REVERT: E 168 LYS cc_start: 0.9422 (mmmt) cc_final: 0.9111 (mmtp) REVERT: E 368 ASP cc_start: 0.7544 (m-30) cc_final: 0.6989 (m-30) REVERT: E 377 ASN cc_start: 0.8791 (p0) cc_final: 0.8541 (p0) REVERT: F 586 TYR cc_start: 0.8935 (t80) cc_final: 0.8594 (t80) REVERT: F 588 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8469 (tp-100) REVERT: F 652 GLN cc_start: 0.8170 (tp40) cc_final: 0.7843 (tp40) REVERT: G 10 GLU cc_start: 0.8306 (pm20) cc_final: 0.8076 (pm20) REVERT: G 66 ARG cc_start: 0.9036 (ttt90) cc_final: 0.8816 (ttt90) REVERT: G 100 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7585 (ttt90) REVERT: H 24 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8339 (ttm110) REVERT: O 29 MET cc_start: 0.6121 (tpt) cc_final: 0.5758 (tpp) REVERT: O 100 MET cc_start: 0.8299 (mpp) cc_final: 0.7580 (mpp) REVERT: P 35 TRP cc_start: 0.7241 (m100) cc_final: 0.6934 (m100) REVERT: I 99 ASN cc_start: 0.8835 (t0) cc_final: 0.8603 (t0) REVERT: I 103 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8121 (mm-40) REVERT: I 107 ASP cc_start: 0.8731 (m-30) cc_final: 0.8510 (m-30) REVERT: I 168 LYS cc_start: 0.9283 (mmmt) cc_final: 0.8937 (mmtp) REVERT: I 368 ASP cc_start: 0.7522 (m-30) cc_final: 0.7042 (m-30) REVERT: I 377 ASN cc_start: 0.8593 (p0) cc_final: 0.8368 (p0) REVERT: K 100 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7605 (ttt180) REVERT: L 4 MET cc_start: 0.8151 (ttt) cc_final: 0.7818 (ttt) REVERT: L 24 ARG cc_start: 0.8359 (ttm110) cc_final: 0.7937 (ttm110) REVERT: Q 74 SER cc_start: 0.7639 (p) cc_final: 0.7299 (m) REVERT: R 97 SER cc_start: 0.9412 (t) cc_final: 0.9154 (t) outliers start: 91 outliers final: 54 residues processed: 575 average time/residue: 0.3488 time to fit residues: 324.0277 Evaluate side-chains 536 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 480 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 62 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 299 optimal weight: 6.9990 chunk 274 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 GLN N 52 GLN E 92 ASN E 302 ASN I 302 ASN K 43 GLN R 26 GLN R 52 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115814 restraints weight = 42105.521| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.26 r_work: 0.3309 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 27672 Z= 0.218 Angle : 0.846 16.764 37929 Z= 0.383 Chirality : 0.053 0.504 4707 Planarity : 0.006 0.148 4446 Dihedral : 13.727 99.498 7234 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.25 % Favored : 91.06 % Rotamer: Outliers : 5.02 % Allowed : 18.25 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3054 helix: 1.11 (0.26), residues: 435 sheet: -0.74 (0.17), residues: 930 loop : -1.76 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS E 249 PHE 0.015 0.002 PHE J 592 TYR 0.018 0.002 TYR R 49 ARG 0.007 0.001 ARG M 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 72) link_NAG-ASN : angle 4.46255 ( 216) link_ALPHA1-6 : bond 0.00552 ( 21) link_ALPHA1-6 : angle 1.84941 ( 63) link_BETA1-4 : bond 0.00425 ( 51) link_BETA1-4 : angle 2.09517 ( 153) link_ALPHA1-2 : bond 0.00885 ( 27) link_ALPHA1-2 : angle 2.10865 ( 81) link_ALPHA1-3 : bond 0.00946 ( 21) link_ALPHA1-3 : angle 2.23167 ( 63) hydrogen bonds : bond 0.04560 ( 708) hydrogen bonds : angle 5.69465 ( 1836) SS BOND : bond 0.00558 ( 45) SS BOND : angle 1.51197 ( 90) covalent geometry : bond 0.00497 (27435) covalent geometry : angle 0.75169 (37263) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 490 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8823 (m-30) cc_final: 0.8343 (m-30) REVERT: C 100 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7719 (ttt180) REVERT: D 77 ASN cc_start: 0.8299 (t0) cc_final: 0.8072 (t0) REVERT: N 35 TRP cc_start: 0.7913 (m100) cc_final: 0.7587 (m100) REVERT: N 47 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8474 (mm) REVERT: E 168 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9147 (mmtp) REVERT: F 588 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8441 (tp-100) REVERT: G 10 GLU cc_start: 0.8483 (pm20) cc_final: 0.8056 (pm20) REVERT: G 100 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.7793 (ttt90) REVERT: H 24 ARG cc_start: 0.8834 (ttm110) cc_final: 0.8442 (ttm110) REVERT: P 35 TRP cc_start: 0.7369 (m100) cc_final: 0.7145 (m100) REVERT: I 99 ASN cc_start: 0.8855 (t0) cc_final: 0.8578 (t0) REVERT: I 103 GLN cc_start: 0.8691 (mm-40) cc_final: 0.7928 (mm-40) REVERT: I 107 ASP cc_start: 0.8755 (m-30) cc_final: 0.8516 (m-30) REVERT: I 381 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7671 (mt-10) REVERT: K 66 ARG cc_start: 0.8913 (ttt90) cc_final: 0.8465 (ttt90) REVERT: K 100 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7730 (ttt180) REVERT: L 20 ARG cc_start: 0.8626 (tpp-160) cc_final: 0.8236 (mmt-90) REVERT: L 24 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8163 (ttm110) REVERT: L 100 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8714 (mm-40) REVERT: R 50 ASN cc_start: 0.7382 (t0) cc_final: 0.7157 (t0) REVERT: R 97 SER cc_start: 0.9508 (t) cc_final: 0.9258 (t) outliers start: 135 outliers final: 103 residues processed: 576 average time/residue: 0.3539 time to fit residues: 327.9630 Evaluate side-chains 570 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 466 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 PRO Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 305 optimal weight: 0.3980 chunk 255 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN D 3 GLN E 92 ASN E 258 GLN P 52 GLN I 302 ASN R 26 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.162744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118305 restraints weight = 41859.291| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.24 r_work: 0.3349 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27672 Z= 0.147 Angle : 0.796 15.728 37929 Z= 0.358 Chirality : 0.050 0.446 4707 Planarity : 0.005 0.147 4446 Dihedral : 13.214 104.288 7230 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.24 % Favored : 92.24 % Rotamer: Outliers : 4.16 % Allowed : 20.96 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.43 (0.15), residues: 3054 helix: 1.32 (0.26), residues: 432 sheet: -0.82 (0.17), residues: 960 loop : -1.68 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS A 249 PHE 0.009 0.001 PHE A 233 TYR 0.016 0.001 TYR C 47 ARG 0.004 0.000 ARG D 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 72) link_NAG-ASN : angle 4.28349 ( 216) link_ALPHA1-6 : bond 0.00642 ( 21) link_ALPHA1-6 : angle 1.82323 ( 63) link_BETA1-4 : bond 0.00463 ( 51) link_BETA1-4 : angle 1.89837 ( 153) link_ALPHA1-2 : bond 0.00928 ( 27) link_ALPHA1-2 : angle 1.89487 ( 81) link_ALPHA1-3 : bond 0.01113 ( 21) link_ALPHA1-3 : angle 2.06941 ( 63) hydrogen bonds : bond 0.04146 ( 708) hydrogen bonds : angle 5.45879 ( 1836) SS BOND : bond 0.00480 ( 45) SS BOND : angle 1.20362 ( 90) covalent geometry : bond 0.00320 (27435) covalent geometry : angle 0.70645 (37263) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 520 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8798 (m-30) cc_final: 0.8274 (m-30) REVERT: B 652 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7920 (tp40) REVERT: C 100 ARG cc_start: 0.8139 (mtp-110) cc_final: 0.7708 (ttt180) REVERT: D 42 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7656 (pttp) REVERT: D 77 ASN cc_start: 0.8396 (t0) cc_final: 0.8148 (t0) REVERT: M 97 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8186 (ttp80) REVERT: N 35 TRP cc_start: 0.7725 (m100) cc_final: 0.7410 (m100) REVERT: N 47 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8267 (mm) REVERT: E 168 LYS cc_start: 0.9443 (mmmt) cc_final: 0.9178 (mmtp) REVERT: E 377 ASN cc_start: 0.8861 (p0) cc_final: 0.8639 (p0) REVERT: F 586 TYR cc_start: 0.8986 (t80) cc_final: 0.8658 (t80) REVERT: F 588 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8377 (tp-100) REVERT: F 603 ILE cc_start: 0.9407 (mm) cc_final: 0.9201 (mt) REVERT: G 100 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7620 (ttt90) REVERT: H 24 ARG cc_start: 0.8799 (ttm110) cc_final: 0.8402 (ttm110) REVERT: O 100 MET cc_start: 0.8421 (mpp) cc_final: 0.7579 (mpp) REVERT: P 35 TRP cc_start: 0.7365 (m100) cc_final: 0.7157 (m100) REVERT: I 99 ASN cc_start: 0.8816 (t0) cc_final: 0.8565 (t0) REVERT: I 103 GLN cc_start: 0.8678 (mm-40) cc_final: 0.7898 (mm-40) REVERT: I 107 ASP cc_start: 0.8739 (m-30) cc_final: 0.8513 (m-30) REVERT: I 168 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9088 (mmtp) REVERT: I 377 ASN cc_start: 0.8743 (p0) cc_final: 0.8490 (p0) REVERT: K 66 ARG cc_start: 0.8871 (ttt90) cc_final: 0.8329 (ttt90) REVERT: K 100 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7697 (ttt90) REVERT: Q 29 MET cc_start: 0.5463 (tpt) cc_final: 0.5163 (tpt) REVERT: R 50 ASN cc_start: 0.7477 (t0) cc_final: 0.7216 (t0) REVERT: R 97 SER cc_start: 0.9517 (t) cc_final: 0.9274 (t) outliers start: 112 outliers final: 83 residues processed: 590 average time/residue: 0.3616 time to fit residues: 345.1056 Evaluate side-chains 571 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 485 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 PRO Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 196 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 172 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN G 3 HIS P 26 GLN I 302 ASN K 3 HIS R 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.116956 restraints weight = 41859.321| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.24 r_work: 0.3329 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27672 Z= 0.163 Angle : 0.793 16.112 37929 Z= 0.357 Chirality : 0.051 0.449 4707 Planarity : 0.005 0.159 4446 Dihedral : 12.698 108.782 7227 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.99 % Favored : 91.52 % Rotamer: Outliers : 5.05 % Allowed : 21.33 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.37 (0.15), residues: 3054 helix: 1.39 (0.26), residues: 432 sheet: -0.77 (0.17), residues: 903 loop : -1.64 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.003 0.001 HIS K 100F PHE 0.009 0.001 PHE A 233 TYR 0.017 0.001 TYR N 49 ARG 0.004 0.000 ARG D 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 72) link_NAG-ASN : angle 4.23331 ( 216) link_ALPHA1-6 : bond 0.00599 ( 21) link_ALPHA1-6 : angle 1.84052 ( 63) link_BETA1-4 : bond 0.00418 ( 51) link_BETA1-4 : angle 1.85405 ( 153) link_ALPHA1-2 : bond 0.00938 ( 27) link_ALPHA1-2 : angle 1.97030 ( 81) link_ALPHA1-3 : bond 0.01013 ( 21) link_ALPHA1-3 : angle 2.08462 ( 63) hydrogen bonds : bond 0.04119 ( 708) hydrogen bonds : angle 5.41059 ( 1836) SS BOND : bond 0.00571 ( 45) SS BOND : angle 1.22964 ( 90) covalent geometry : bond 0.00368 (27435) covalent geometry : angle 0.70506 (37263) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 493 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8791 (m-30) cc_final: 0.8307 (m-30) REVERT: B 652 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: C 100 ARG cc_start: 0.8156 (mtp-110) cc_final: 0.7746 (ttt180) REVERT: D 42 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7612 (ptpt) REVERT: D 77 ASN cc_start: 0.8543 (t0) cc_final: 0.8306 (t0) REVERT: M 97 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8187 (ttp80) REVERT: N 35 TRP cc_start: 0.7859 (m100) cc_final: 0.7653 (m100) REVERT: N 47 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8402 (mm) REVERT: E 168 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9189 (mmtp) REVERT: E 377 ASN cc_start: 0.8885 (p0) cc_final: 0.8649 (p0) REVERT: F 588 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8380 (tp-100) REVERT: G 100 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.7643 (ttt90) REVERT: P 35 TRP cc_start: 0.7504 (m100) cc_final: 0.7225 (m100) REVERT: I 99 ASN cc_start: 0.8826 (t0) cc_final: 0.8495 (t0) REVERT: I 107 ASP cc_start: 0.8761 (m-30) cc_final: 0.8499 (m-30) REVERT: I 377 ASN cc_start: 0.8752 (p0) cc_final: 0.8481 (p0) REVERT: K 100 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7770 (ttt90) REVERT: Q 29 MET cc_start: 0.5524 (tpt) cc_final: 0.5311 (tpt) REVERT: R 97 SER cc_start: 0.9551 (t) cc_final: 0.9319 (t) outliers start: 136 outliers final: 101 residues processed: 587 average time/residue: 0.3378 time to fit residues: 321.7943 Evaluate side-chains 581 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 477 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 269 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN P 26 GLN I 92 ASN I 105 HIS I 258 GLN I 302 ASN R 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111683 restraints weight = 41653.906| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.17 r_work: 0.3246 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 27672 Z= 0.250 Angle : 0.875 17.111 37929 Z= 0.397 Chirality : 0.053 0.490 4707 Planarity : 0.006 0.155 4446 Dihedral : 12.677 110.576 7227 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.02 % Favored : 91.42 % Rotamer: Outliers : 5.91 % Allowed : 21.11 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.40 (0.15), residues: 3054 helix: 1.05 (0.26), residues: 453 sheet: -0.67 (0.17), residues: 900 loop : -1.67 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 112 HIS 0.005 0.001 HIS P 38 PHE 0.017 0.002 PHE E 383 TYR 0.016 0.002 TYR E 384 ARG 0.005 0.001 ARG I 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 72) link_NAG-ASN : angle 4.61122 ( 216) link_ALPHA1-6 : bond 0.00485 ( 21) link_ALPHA1-6 : angle 1.83009 ( 63) link_BETA1-4 : bond 0.00433 ( 51) link_BETA1-4 : angle 2.14859 ( 153) link_ALPHA1-2 : bond 0.00963 ( 27) link_ALPHA1-2 : angle 2.10806 ( 81) link_ALPHA1-3 : bond 0.00817 ( 21) link_ALPHA1-3 : angle 2.13581 ( 63) hydrogen bonds : bond 0.04744 ( 708) hydrogen bonds : angle 5.75433 ( 1836) SS BOND : bond 0.00697 ( 45) SS BOND : angle 1.83875 ( 90) covalent geometry : bond 0.00583 (27435) covalent geometry : angle 0.77783 (37263) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 478 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7314 (t0) cc_final: 0.7068 (t0) REVERT: B 530 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7987 (mtp) REVERT: C 100 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7806 (ttt180) REVERT: D 42 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7729 (ptpt) REVERT: D 77 ASN cc_start: 0.8640 (t0) cc_final: 0.8407 (t0) REVERT: M 97 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8267 (ttp80) REVERT: N 35 TRP cc_start: 0.8087 (m100) cc_final: 0.7675 (m100) REVERT: N 47 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8476 (mm) REVERT: E 168 LYS cc_start: 0.9389 (mmmt) cc_final: 0.9171 (mmtp) REVERT: E 420 ILE cc_start: 0.8681 (tt) cc_final: 0.8475 (mt) REVERT: G 100 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7721 (ttt90) REVERT: H 20 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8262 (mmt90) REVERT: I 99 ASN cc_start: 0.8854 (t0) cc_final: 0.8508 (t0) REVERT: I 107 ASP cc_start: 0.8781 (m-30) cc_final: 0.8520 (m-30) REVERT: J 530 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: K 100 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7836 (ttt90) REVERT: L 77 ASN cc_start: 0.8672 (t0) cc_final: 0.8467 (t0) REVERT: Q 32 TYR cc_start: 0.7208 (p90) cc_final: 0.6629 (p90) REVERT: R 97 SER cc_start: 0.9581 (t) cc_final: 0.9375 (t) outliers start: 159 outliers final: 126 residues processed: 583 average time/residue: 0.3390 time to fit residues: 321.3324 Evaluate side-chains 580 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 450 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 26 GLN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 139 optimal weight: 0.0870 chunk 171 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 3 HIS E 92 ASN F 590 GLN I 92 ASN I 302 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100630 restraints weight = 40013.487| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.75 r_work: 0.3012 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27672 Z= 0.138 Angle : 0.801 17.706 37929 Z= 0.361 Chirality : 0.050 0.424 4707 Planarity : 0.006 0.169 4446 Dihedral : 12.097 106.652 7227 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.56 % Favored : 91.88 % Rotamer: Outliers : 3.98 % Allowed : 22.82 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.28 (0.15), residues: 3054 helix: 1.25 (0.25), residues: 450 sheet: -0.56 (0.17), residues: 882 loop : -1.63 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 35 HIS 0.003 0.001 HIS K 100F PHE 0.009 0.001 PHE M 100K TYR 0.016 0.001 TYR C 47 ARG 0.007 0.000 ARG H 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 72) link_NAG-ASN : angle 4.24283 ( 216) link_ALPHA1-6 : bond 0.00605 ( 21) link_ALPHA1-6 : angle 1.78035 ( 63) link_BETA1-4 : bond 0.00494 ( 51) link_BETA1-4 : angle 1.82251 ( 153) link_ALPHA1-2 : bond 0.00928 ( 27) link_ALPHA1-2 : angle 1.83506 ( 81) link_ALPHA1-3 : bond 0.00958 ( 21) link_ALPHA1-3 : angle 1.96135 ( 63) hydrogen bonds : bond 0.04084 ( 708) hydrogen bonds : angle 5.50363 ( 1836) SS BOND : bond 0.00466 ( 45) SS BOND : angle 1.49032 ( 90) covalent geometry : bond 0.00301 (27435) covalent geometry : angle 0.71463 (37263) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 496 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8917 (m-30) cc_final: 0.8615 (m-30) REVERT: C 100 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.8026 (ttt180) REVERT: D 77 ASN cc_start: 0.8684 (t0) cc_final: 0.8466 (t0) REVERT: G 100 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7830 (ttt90) REVERT: G 100 LEU cc_start: 0.9320 (mt) cc_final: 0.9058 (mt) REVERT: H 20 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8241 (mmt90) REVERT: I 99 ASN cc_start: 0.8938 (t0) cc_final: 0.8657 (t0) REVERT: I 377 ASN cc_start: 0.8978 (p0) cc_final: 0.8733 (p0) REVERT: K 100 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7910 (ttt90) REVERT: L 77 ASN cc_start: 0.8767 (t0) cc_final: 0.8552 (t0) REVERT: Q 32 TYR cc_start: 0.7370 (p90) cc_final: 0.6828 (p90) REVERT: R 60 GLU cc_start: 0.8586 (pp20) cc_final: 0.7846 (pp20) outliers start: 107 outliers final: 95 residues processed: 565 average time/residue: 0.3515 time to fit residues: 322.6082 Evaluate side-chains 564 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 469 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 36 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 222 optimal weight: 0.5980 chunk 160 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 428 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN E 92 ASN I 92 ASN I 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101057 restraints weight = 40214.612| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.80 r_work: 0.3007 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27672 Z= 0.147 Angle : 0.786 15.606 37929 Z= 0.354 Chirality : 0.049 0.423 4707 Planarity : 0.005 0.153 4446 Dihedral : 11.699 101.517 7227 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.73 % Favored : 91.85 % Rotamer: Outliers : 4.09 % Allowed : 22.97 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.28 (0.15), residues: 3054 helix: 1.45 (0.26), residues: 432 sheet: -0.60 (0.18), residues: 855 loop : -1.62 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 35 HIS 0.004 0.001 HIS K 100F PHE 0.007 0.001 PHE M 100K TYR 0.015 0.001 TYR C 47 ARG 0.006 0.000 ARG H 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 72) link_NAG-ASN : angle 4.17842 ( 216) link_ALPHA1-6 : bond 0.00566 ( 21) link_ALPHA1-6 : angle 1.80982 ( 63) link_BETA1-4 : bond 0.00453 ( 51) link_BETA1-4 : angle 1.85792 ( 153) link_ALPHA1-2 : bond 0.00929 ( 27) link_ALPHA1-2 : angle 1.86274 ( 81) link_ALPHA1-3 : bond 0.00873 ( 21) link_ALPHA1-3 : angle 1.94538 ( 63) hydrogen bonds : bond 0.04052 ( 708) hydrogen bonds : angle 5.40753 ( 1836) SS BOND : bond 0.00514 ( 45) SS BOND : angle 1.39977 ( 90) covalent geometry : bond 0.00331 (27435) covalent geometry : angle 0.69985 (37263) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 486 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8908 (m-30) cc_final: 0.8541 (m-30) REVERT: C 100 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.8056 (ttt180) REVERT: D 77 ASN cc_start: 0.8709 (t0) cc_final: 0.8492 (t0) REVERT: E 161 MET cc_start: 0.8912 (tpt) cc_final: 0.8553 (tpp) REVERT: G 100 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.7839 (ttt90) REVERT: H 20 ARG cc_start: 0.8623 (tpp-160) cc_final: 0.8260 (mmt90) REVERT: I 99 ASN cc_start: 0.8926 (t0) cc_final: 0.8647 (t0) REVERT: I 377 ASN cc_start: 0.8943 (p0) cc_final: 0.8742 (p0) REVERT: K 100 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.8066 (ttt180) REVERT: L 77 ASN cc_start: 0.8774 (t0) cc_final: 0.8556 (t0) REVERT: Q 32 TYR cc_start: 0.7321 (p90) cc_final: 0.6743 (p90) REVERT: R 60 GLU cc_start: 0.8581 (pp20) cc_final: 0.7787 (pp20) outliers start: 110 outliers final: 95 residues processed: 553 average time/residue: 0.3431 time to fit residues: 307.9027 Evaluate side-chains 569 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 474 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 281 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 247 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 198 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN I 92 ASN I 258 GLN I 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101851 restraints weight = 39895.183| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.73 r_work: 0.3033 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27672 Z= 0.137 Angle : 0.772 15.327 37929 Z= 0.349 Chirality : 0.049 0.410 4707 Planarity : 0.005 0.144 4446 Dihedral : 11.344 97.003 7227 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.43 % Favored : 92.21 % Rotamer: Outliers : 3.64 % Allowed : 23.75 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.24 (0.15), residues: 3054 helix: 1.32 (0.26), residues: 450 sheet: -0.55 (0.18), residues: 855 loop : -1.58 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 96 HIS 0.004 0.001 HIS N 38 PHE 0.007 0.001 PHE M 100K TYR 0.015 0.001 TYR C 47 ARG 0.005 0.000 ARG H 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 72) link_NAG-ASN : angle 4.07058 ( 216) link_ALPHA1-6 : bond 0.00584 ( 21) link_ALPHA1-6 : angle 1.77433 ( 63) link_BETA1-4 : bond 0.00473 ( 51) link_BETA1-4 : angle 1.79875 ( 153) link_ALPHA1-2 : bond 0.00965 ( 27) link_ALPHA1-2 : angle 1.81277 ( 81) link_ALPHA1-3 : bond 0.00866 ( 21) link_ALPHA1-3 : angle 1.90024 ( 63) hydrogen bonds : bond 0.03890 ( 708) hydrogen bonds : angle 5.33275 ( 1836) SS BOND : bond 0.00480 ( 45) SS BOND : angle 1.19974 ( 90) covalent geometry : bond 0.00304 (27435) covalent geometry : angle 0.68924 (37263) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 479 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8870 (m-30) cc_final: 0.8539 (m-30) REVERT: B 588 GLN cc_start: 0.8906 (tp40) cc_final: 0.8664 (tt0) REVERT: C 100 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.8047 (ttt180) REVERT: D 24 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8393 (ttm-80) REVERT: D 77 ASN cc_start: 0.8715 (t0) cc_final: 0.8511 (t0) REVERT: F 588 GLN cc_start: 0.8923 (tp40) cc_final: 0.8527 (tt0) REVERT: G 100 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7856 (ttt90) REVERT: H 20 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8250 (mmt90) REVERT: O 100 MET cc_start: 0.8358 (mpp) cc_final: 0.7958 (mmm) REVERT: I 99 ASN cc_start: 0.8932 (t0) cc_final: 0.8653 (t0) REVERT: I 199 SER cc_start: 0.9278 (p) cc_final: 0.9057 (t) REVERT: J 588 GLN cc_start: 0.8914 (tp40) cc_final: 0.8603 (tt0) REVERT: K 100 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.8042 (ttt180) REVERT: L 77 ASN cc_start: 0.8799 (t0) cc_final: 0.8597 (t0) REVERT: R 60 GLU cc_start: 0.8561 (pp20) cc_final: 0.7760 (pp20) outliers start: 98 outliers final: 89 residues processed: 542 average time/residue: 0.3436 time to fit residues: 303.8402 Evaluate side-chains 549 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 460 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 157 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 165 optimal weight: 0.0010 chunk 190 optimal weight: 3.9990 chunk 241 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN N 37 GLN E 92 ASN I 92 ASN ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102786 restraints weight = 40122.643| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.82 r_work: 0.3027 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27672 Z= 0.133 Angle : 0.759 15.203 37929 Z= 0.345 Chirality : 0.049 0.405 4707 Planarity : 0.005 0.137 4446 Dihedral : 11.060 91.757 7227 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.50 % Favored : 92.08 % Rotamer: Outliers : 3.53 % Allowed : 23.97 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -1.23 (0.15), residues: 3054 helix: 1.30 (0.26), residues: 450 sheet: -0.55 (0.18), residues: 855 loop : -1.57 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 96 HIS 0.004 0.001 HIS K 100F PHE 0.008 0.001 PHE M 100K TYR 0.015 0.001 TYR I 330 ARG 0.005 0.000 ARG H 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 72) link_NAG-ASN : angle 3.99420 ( 216) link_ALPHA1-6 : bond 0.00601 ( 21) link_ALPHA1-6 : angle 1.75025 ( 63) link_BETA1-4 : bond 0.00469 ( 51) link_BETA1-4 : angle 1.77214 ( 153) link_ALPHA1-2 : bond 0.00966 ( 27) link_ALPHA1-2 : angle 1.76862 ( 81) link_ALPHA1-3 : bond 0.00856 ( 21) link_ALPHA1-3 : angle 1.85895 ( 63) hydrogen bonds : bond 0.03829 ( 708) hydrogen bonds : angle 5.26646 ( 1836) SS BOND : bond 0.00484 ( 45) SS BOND : angle 1.17192 ( 90) covalent geometry : bond 0.00293 (27435) covalent geometry : angle 0.67845 (37263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14216.94 seconds wall clock time: 248 minutes 5.61 seconds (14885.61 seconds total)