Starting phenix.real_space_refine on Sat Jul 4 14:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fr6_29396/07_2026/8fr6_29396.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 129 5.16 5 C 13248 2.51 5 N 3426 2.21 5 O 4434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21237 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "I" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "J" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} 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 chiralities: 2 Chain: "N" 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 chiralities: 5 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 chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" 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 chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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 chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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 chiralities: 5 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 chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" 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 chiralities: 6 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" 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 chiralities: 5 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" 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 chiralities: 5 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 chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "y" 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 chiralities: 5 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 3 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.11, per 1000 atoms: 0.19 Number of scatterers: 21237 At special positions: 0 Unit cell: (154.38, 146.08, 126.16, 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 129 16.00 O 4434 8.00 N 3426 7.00 C 13248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.05 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " 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=2.03 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 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 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 D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN e 4 " - " MAN e 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA k 3 " - " MAN k 4 " " BMA p 3 " - " MAN p 4 " " BMA s 3 " - " MAN s 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 6 " " BMA W 3 " - " MAN W 5 " " BMA b 3 " - " MAN b 5 " " BMA e 3 " - " MAN e 6 " " BMA k 3 " - " MAN k 5 " " BMA p 3 " - " MAN p 5 " " BMA s 3 " - " MAN s 6 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " 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-ASN " NAG 0 1 " - " ASN I 160 " " NAG 1 1 " - " ASN I 392 " " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 137 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 355 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 137 " " NAG G 603 " - " ASN G 339 " " NAG G 604 " - " ASN G 355 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 137 " " NAG I 603 " - " ASN I 339 " " NAG I 604 " - " ASN I 355 " " NAG M 1 " - " ASN C 133 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 197 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 276 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 160 " " NAG Z 1 " - " ASN C 392 " " NAG a 1 " - " ASN G 133 " " NAG b 1 " - " ASN G 156 " " NAG c 1 " - " ASN G 197 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 262 " " NAG f 1 " - " ASN G 276 " " NAG g 1 " - " ASN G 295 " " NAG h 1 " - " ASN G 301 " " NAG i 1 " - " ASN G 332 " " NAG j 1 " - " ASN G 363 " " NAG k 1 " - " ASN G 386 " " NAG l 1 " - " ASN G 448 " " NAG m 1 " - " ASN G 160 " " NAG n 1 " - " ASN G 392 " " NAG o 1 " - " ASN I 133 " " NAG p 1 " - " ASN I 156 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 234 " " NAG s 1 " - " ASN I 262 " " NAG t 1 " - " ASN I 276 " " NAG u 1 " - " ASN I 295 " " NAG v 1 " - " ASN I 301 " " NAG w 1 " - " ASN I 332 " " NAG x 1 " - " ASN I 363 " " NAG y 1 " - " ASN I 386 " " NAG z 1 " - " ASN I 448 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 795.8 milliseconds 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 21.4% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 544 removed outlier: 4.101A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.102A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.737A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.897A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.255A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.852A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 520 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 4.102A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.736A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.897A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.255A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.851A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 101 through 115 Processing helix chain 'I' and resid 139 through 151 removed outlier: 3.737A pdb=" N ARG I 151 " --> pdb=" O ASP I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 354 removed outlier: 3.897A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 425 through 429 removed outlier: 4.255A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 3.851A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.251A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.252A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.325A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 177 removed outlier: 4.562A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.364A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.189A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.483A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.264A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.904A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 121 through 122 removed outlier: 4.325A pdb=" N CYS G 201 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 169 through 177 removed outlier: 4.563A pdb=" N GLU G 190 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.364A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.190A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.190A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.484A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 121 through 122 removed outlier: 4.325A pdb=" N CYS I 201 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 169 through 177 removed outlier: 4.562A pdb=" N GLU I 190 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 260 through 261 removed outlier: 6.364A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.190A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 271 through 273 removed outlier: 11.190A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.483A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.310A pdb=" N GLU D 10 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.239A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.310A pdb=" N GLU H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.239A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.310A pdb=" N GLU J 10 " --> pdb=" O ILE J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.238A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 14 removed outlier: 4.394A pdb=" N GLY K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 14 removed outlier: 4.394A pdb=" N GLY K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN K 90 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2178 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: 3.20 Time building geometry restraints manager: 2.68 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: 6386 1.34 - 1.47: 5725 1.47 - 1.59: 9354 1.59 - 1.72: 0 1.72 - 1.85: 174 Bond restraints: 21639 Sorted by residual: bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.44e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" N ARG C 500 " pdb=" CA ARG C 500 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.44e-02 4.82e+03 4.69e+00 bond pdb=" N ARG I 500 " pdb=" CA ARG I 500 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.44e-02 4.82e+03 4.65e+00 ... (remaining 21634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 27657 1.42 - 2.83: 1204 2.83 - 4.25: 306 4.25 - 5.67: 134 5.67 - 7.08: 63 Bond angle restraints: 29364 Sorted by residual: angle pdb=" C ARG G 500 " pdb=" CA ARG G 500 " pdb=" CB ARG G 500 " ideal model delta sigma weight residual 110.72 103.64 7.08 1.77e+00 3.19e-01 1.60e+01 angle pdb=" C ARG I 500 " pdb=" CA ARG I 500 " pdb=" CB ARG I 500 " ideal model delta sigma weight residual 110.72 103.64 7.08 1.77e+00 3.19e-01 1.60e+01 angle pdb=" C ARG C 500 " pdb=" CA ARG C 500 " pdb=" CB ARG C 500 " ideal model delta sigma weight residual 110.72 103.66 7.06 1.77e+00 3.19e-01 1.59e+01 angle pdb=" N CYS I 501 " pdb=" CA CYS I 501 " pdb=" C CYS I 501 " ideal model delta sigma weight residual 110.48 115.13 -4.65 1.48e+00 4.57e-01 9.87e+00 angle pdb=" N CYS G 501 " pdb=" CA CYS G 501 " pdb=" C CYS G 501 " ideal model delta sigma weight residual 110.48 115.11 -4.63 1.48e+00 4.57e-01 9.79e+00 ... (remaining 29359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 10216 17.91 - 35.83: 1123 35.83 - 53.74: 317 53.74 - 71.66: 89 71.66 - 89.57: 21 Dihedral angle restraints: 11766 sinusoidal: 4719 harmonic: 7047 Sorted by residual: dihedral pdb=" CB CYS F 605 " pdb=" SG CYS F 605 " pdb=" SG CYS I 501 " pdb=" CB CYS I 501 " ideal model delta sinusoidal sigma weight residual 93.00 39.22 53.78 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CB CYS A 605 " pdb=" SG CYS A 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual 93.00 39.38 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS B 605 " pdb=" SG CYS B 605 " pdb=" SG CYS G 501 " pdb=" CB CYS G 501 " ideal model delta sinusoidal sigma weight residual 93.00 39.38 53.62 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 11763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3136 0.059 - 0.119: 504 0.119 - 0.178: 98 0.178 - 0.237: 3 0.237 - 0.296: 33 Chirality restraints: 3774 Sorted by residual: chirality pdb=" C5 BMA y 3 " pdb=" C4 BMA y 3 " pdb=" C6 BMA y 3 " pdb=" O5 BMA y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C5 BMA k 3 " pdb=" C4 BMA k 3 " pdb=" C6 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3771 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 43 " -0.024 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO L 44 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 43 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO K 44 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO K 44 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 44 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 43 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO E 44 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " -0.021 5.00e-02 4.00e+02 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 446 2.68 - 3.24: 20228 3.24 - 3.79: 32574 3.79 - 4.35: 45562 4.35 - 4.90: 73237 Nonbonded interactions: 172047 Sorted by model distance: nonbonded pdb=" O GLN D 1 " pdb=" NE2 GLN D 1 " model vdw 2.125 3.120 nonbonded pdb=" O GLN H 1 " pdb=" NE2 GLN H 1 " model vdw 2.126 3.120 nonbonded pdb=" O GLN J 1 " pdb=" NE2 GLN J 1 " model vdw 2.126 3.120 nonbonded pdb=" OG1 THR C 139 " pdb=" OD1 ASP C 141 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR I 139 " pdb=" OD1 ASP I 141 " model vdw 2.221 3.040 ... (remaining 172042 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: 0.05 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'T' selection = chain 'a' selection = chain 'c' selection = chain 'h' selection = chain 'o' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'b' selection = chain 'k' selection = chain 'p' selection = chain 'y' } ncs_group { reference = chain 'Q' selection = chain 'e' 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: 8.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.250 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.005 0.047 21840 Z= 0.245 Angle : 0.831 10.600 29925 Z= 0.343 Chirality : 0.054 0.296 3774 Planarity : 0.004 0.042 3504 Dihedral : 16.597 89.572 7104 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.98 % Allowed : 20.51 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2406 helix: 0.96 (0.27), residues: 468 sheet: 0.35 (0.19), residues: 732 loop : 0.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 504 TYR 0.011 0.001 TYR E 49 PHE 0.007 0.001 PHE C 53 TRP 0.018 0.001 TRP C 35 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.25 (21639) covalent geometry : angle 0.79221 / 0.33 (29364) SS BOND : bond 0.00408 / 0.28 ( 42) SS BOND : angle 1.04256 / 0.69 ( 84) hydrogen bonds : bond 0.19226 / 12.94 ( 771) hydrogen bonds : angle 8.29329 / 6.12 ( 2178) link_ALPHA1-2 : bond 0.00305 / 0.14 ( 3) link_ALPHA1-2 : angle 1.88420 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00242 / 0.16 ( 9) link_ALPHA1-3 : angle 1.92905 / 1.30 ( 27) link_ALPHA1-6 : bond 0.00525 / 0.36 ( 9) link_ALPHA1-6 : angle 1.53590 / 1.07 ( 27) link_BETA1-4 : bond 0.00658 / 0.43 ( 75) link_BETA1-4 : angle 2.50601 / 1.75 ( 225) link_NAG-ASN : bond 0.00179 / 0.12 ( 63) link_NAG-ASN : angle 1.67912 / 1.23 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.8324 (tp30) cc_final: 0.8113 (tp30) REVERT: G 356 ASN cc_start: 0.8789 (p0) cc_final: 0.8568 (p0) REVERT: I 356 ASN cc_start: 0.8720 (p0) cc_final: 0.8495 (p0) REVERT: D 64 ARG cc_start: 0.7746 (ttp-170) cc_final: 0.7491 (mtm-85) REVERT: H 64 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7567 (mtm-85) REVERT: J 32 TYR cc_start: 0.7785 (m-80) cc_final: 0.7252 (m-80) outliers start: 21 outliers final: 18 residues processed: 301 average time/residue: 0.5337 time to fit residues: 183.5065 Evaluate side-chains 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 GLN A 656 ASN A 658 GLN B 652 GLN B 656 ASN F 652 GLN F 656 ASN F 658 GLN I 411 ASN D 1 GLN D 96 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 96 GLN L 30 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN K 30 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.118683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064644 restraints weight = 40601.454| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.66 r_work: 0.2725 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21840 Z= 0.178 Angle : 0.676 9.172 29925 Z= 0.325 Chirality : 0.044 0.281 3774 Planarity : 0.004 0.044 3504 Dihedral : 4.947 33.687 2648 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.25 % Allowed : 21.30 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2406 helix: 1.28 (0.26), residues: 456 sheet: 0.27 (0.18), residues: 759 loop : 0.16 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 500 TYR 0.026 0.002 TYR H 27 PHE 0.012 0.001 PHE C 53 TRP 0.009 0.001 TRP I 96 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (21639) covalent geometry : angle 0.63345 / 0.32 (29364) SS BOND : bond 0.00313 / 0.22 ( 42) SS BOND : angle 1.11568 / 0.77 ( 84) hydrogen bonds : bond 0.04365 / 2.86 ( 771) hydrogen bonds : angle 5.72915 / 4.22 ( 2178) link_ALPHA1-2 : bond 0.00775 / 0.35 ( 3) link_ALPHA1-2 : angle 1.62546 / 1.00 ( 9) link_ALPHA1-3 : bond 0.00526 / 0.36 ( 9) link_ALPHA1-3 : angle 1.48666 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00687 / 0.47 ( 9) link_ALPHA1-6 : angle 1.50284 / 1.03 ( 27) link_BETA1-4 : bond 0.00696 / 0.47 ( 75) link_BETA1-4 : angle 2.12604 / 1.49 ( 225) link_NAG-ASN : bond 0.00381 / 0.25 ( 63) link_NAG-ASN : angle 1.81938 / 1.33 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8926 (p0) cc_final: 0.8619 (p0) REVERT: G 356 ASN cc_start: 0.8891 (p0) cc_final: 0.8648 (p0) REVERT: I 356 ASN cc_start: 0.8863 (p0) cc_final: 0.8557 (p0) REVERT: D 31 ASP cc_start: 0.8430 (t0) cc_final: 0.8012 (t0) REVERT: D 96 GLN cc_start: 0.7266 (mt0) cc_final: 0.6847 (mt0) REVERT: E 32 TYR cc_start: 0.6406 (m-80) cc_final: 0.5925 (m-80) REVERT: E 75 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4942 (mp) REVERT: H 31 ASP cc_start: 0.8424 (t0) cc_final: 0.8106 (t0) REVERT: H 32 TYR cc_start: 0.7904 (m-80) cc_final: 0.7528 (m-10) REVERT: H 64 ARG cc_start: 0.6353 (ttp-170) cc_final: 0.5930 (mtm-85) REVERT: H 94 ARG cc_start: 0.8374 (ptt180) cc_final: 0.7940 (ptt180) REVERT: H 96 GLN cc_start: 0.7278 (mt0) cc_final: 0.6934 (mt0) REVERT: L 48 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6583 (mm) REVERT: L 75 ILE cc_start: 0.5171 (OUTLIER) cc_final: 0.4783 (mp) REVERT: J 31 ASP cc_start: 0.8554 (t0) cc_final: 0.7877 (t0) REVERT: J 96 GLN cc_start: 0.7315 (tt0) cc_final: 0.6842 (tp-100) REVERT: K 36 TYR cc_start: 0.6776 (m-80) cc_final: 0.6289 (m-80) REVERT: K 48 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6893 (mm) REVERT: K 75 ILE cc_start: 0.5376 (OUTLIER) cc_final: 0.5004 (mp) outliers start: 48 outliers final: 14 residues processed: 286 average time/residue: 0.5036 time to fit residues: 165.7026 Evaluate side-chains 268 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 0.5980 chunk 198 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 227 optimal weight: 30.0000 chunk 196 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN C 94 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 411 ASN D 30 ASN D 43 HIS E 30 ASN J 30 ASN J 43 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.117585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.063537 restraints weight = 40565.259| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.62 r_work: 0.2700 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21840 Z= 0.213 Angle : 0.667 9.718 29925 Z= 0.319 Chirality : 0.044 0.267 3774 Planarity : 0.004 0.044 3504 Dihedral : 4.438 24.890 2620 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.90 % Allowed : 21.86 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2406 helix: 1.31 (0.26), residues: 456 sheet: 0.11 (0.18), residues: 762 loop : 0.15 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 500 TYR 0.027 0.002 TYR L 49 PHE 0.014 0.001 PHE H 63 TRP 0.011 0.001 TRP C 96 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (21639) covalent geometry : angle 0.62242 / 0.31 (29364) SS BOND : bond 0.00298 / 0.22 ( 42) SS BOND : angle 0.92020 / 0.64 ( 84) hydrogen bonds : bond 0.04229 / 2.78 ( 771) hydrogen bonds : angle 5.38537 / 3.98 ( 2178) link_ALPHA1-2 : bond 0.00534 / 0.24 ( 3) link_ALPHA1-2 : angle 1.61311 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00470 / 0.32 ( 9) link_ALPHA1-3 : angle 1.36376 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00669 / 0.46 ( 9) link_ALPHA1-6 : angle 1.40430 / 0.96 ( 27) link_BETA1-4 : bond 0.00660 / 0.45 ( 75) link_BETA1-4 : angle 2.06119 / 1.46 ( 225) link_NAG-ASN : bond 0.00447 / 0.28 ( 63) link_NAG-ASN : angle 2.01881 / 1.47 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8926 (p0) cc_final: 0.8592 (p0) REVERT: G 114 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: G 356 ASN cc_start: 0.8864 (p0) cc_final: 0.8590 (p0) REVERT: I 356 ASN cc_start: 0.8869 (p0) cc_final: 0.8566 (p0) REVERT: D 31 ASP cc_start: 0.8578 (t0) cc_final: 0.8211 (OUTLIER) REVERT: D 32 TYR cc_start: 0.7833 (m-80) cc_final: 0.7331 (m-10) REVERT: D 96 GLN cc_start: 0.7537 (mt0) cc_final: 0.7227 (mt0) REVERT: E 32 TYR cc_start: 0.6558 (m-80) cc_final: 0.6102 (m-80) REVERT: E 58 VAL cc_start: 0.5777 (OUTLIER) cc_final: 0.5538 (p) REVERT: E 75 ILE cc_start: 0.5171 (OUTLIER) cc_final: 0.4840 (mp) REVERT: H 31 ASP cc_start: 0.8531 (t0) cc_final: 0.8072 (t0) REVERT: H 32 TYR cc_start: 0.8024 (m-80) cc_final: 0.7719 (m-10) REVERT: H 39 GLN cc_start: 0.8275 (tp40) cc_final: 0.8030 (tp-100) REVERT: H 64 ARG cc_start: 0.6386 (ttp-170) cc_final: 0.5960 (mtm-85) REVERT: H 96 GLN cc_start: 0.7710 (mt0) cc_final: 0.7318 (mt0) REVERT: L 48 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6842 (mm) REVERT: L 75 ILE cc_start: 0.4770 (OUTLIER) cc_final: 0.4477 (mp) REVERT: J 31 ASP cc_start: 0.8557 (t0) cc_final: 0.8066 (t0) REVERT: J 32 TYR cc_start: 0.8012 (m-80) cc_final: 0.7804 (m-80) REVERT: J 96 GLN cc_start: 0.7511 (tt0) cc_final: 0.7256 (mt0) REVERT: K 48 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6855 (mm) REVERT: K 75 ILE cc_start: 0.5240 (OUTLIER) cc_final: 0.4941 (mp) outliers start: 62 outliers final: 31 residues processed: 286 average time/residue: 0.5098 time to fit residues: 168.0935 Evaluate side-chains 276 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 208 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 215 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 94 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 43 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.118443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.064936 restraints weight = 40615.795| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.60 r_work: 0.2738 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21840 Z= 0.131 Angle : 0.614 9.493 29925 Z= 0.293 Chirality : 0.042 0.258 3774 Planarity : 0.004 0.050 3504 Dihedral : 4.245 18.356 2619 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.20 % Allowed : 23.13 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2406 helix: 1.43 (0.26), residues: 459 sheet: 0.13 (0.18), residues: 753 loop : 0.20 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.029 0.002 TYR H 27 PHE 0.014 0.001 PHE C 53 TRP 0.009 0.001 TRP C 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21639) covalent geometry : angle 0.57312 / 0.28 (29364) SS BOND : bond 0.00249 / 0.18 ( 42) SS BOND : angle 0.77877 / 0.54 ( 84) hydrogen bonds : bond 0.03485 / 2.28 ( 771) hydrogen bonds : angle 5.08859 / 3.75 ( 2178) link_ALPHA1-2 : bond 0.00596 / 0.27 ( 3) link_ALPHA1-2 : angle 1.59612 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00454 / 0.31 ( 9) link_ALPHA1-3 : angle 1.38987 / 0.97 ( 27) link_ALPHA1-6 : bond 0.00636 / 0.44 ( 9) link_ALPHA1-6 : angle 1.39844 / 0.96 ( 27) link_BETA1-4 : bond 0.00633 / 0.43 ( 75) link_BETA1-4 : angle 1.91647 / 1.36 ( 225) link_NAG-ASN : bond 0.00261 / 0.17 ( 63) link_NAG-ASN : angle 1.84138 / 1.36 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8877 (p0) cc_final: 0.8541 (p0) REVERT: C 416 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8155 (pp) REVERT: G 114 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: G 356 ASN cc_start: 0.8825 (p0) cc_final: 0.8549 (p0) REVERT: I 356 ASN cc_start: 0.8836 (p0) cc_final: 0.8532 (p0) REVERT: D 28 LYS cc_start: 0.8281 (pmtt) cc_final: 0.7945 (ptmm) REVERT: D 31 ASP cc_start: 0.8617 (t0) cc_final: 0.8284 (p0) REVERT: D 32 TYR cc_start: 0.7863 (m-80) cc_final: 0.7523 (m-10) REVERT: E 30 ASN cc_start: 0.6251 (t0) cc_final: 0.5735 (t0) REVERT: E 32 TYR cc_start: 0.6723 (m-80) cc_final: 0.6023 (m-80) REVERT: H 39 GLN cc_start: 0.8379 (tp40) cc_final: 0.8141 (tp40) REVERT: H 64 ARG cc_start: 0.6333 (ttp-170) cc_final: 0.5907 (mtm-85) REVERT: H 95 LEU cc_start: 0.8485 (tp) cc_final: 0.8129 (tm) REVERT: H 96 GLN cc_start: 0.7800 (mt0) cc_final: 0.7495 (mt0) REVERT: L 32 TYR cc_start: 0.6664 (m-80) cc_final: 0.5891 (m-80) REVERT: L 48 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6837 (mm) REVERT: L 75 ILE cc_start: 0.4716 (OUTLIER) cc_final: 0.4395 (mp) REVERT: L 93 HIS cc_start: 0.8559 (m90) cc_final: 0.8224 (m-70) REVERT: J 31 ASP cc_start: 0.8578 (t0) cc_final: 0.8180 (t0) REVERT: J 32 TYR cc_start: 0.8005 (m-80) cc_final: 0.7652 (m-80) REVERT: J 96 GLN cc_start: 0.7619 (tt0) cc_final: 0.7086 (tp40) REVERT: K 30 ASN cc_start: 0.6531 (t0) cc_final: 0.6093 (t0) REVERT: K 48 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6923 (mm) outliers start: 47 outliers final: 30 residues processed: 283 average time/residue: 0.5764 time to fit residues: 187.1619 Evaluate side-chains 281 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 87 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN D 96 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.118355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064934 restraints weight = 40341.994| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.56 r_work: 0.2738 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21840 Z= 0.137 Angle : 0.615 9.580 29925 Z= 0.294 Chirality : 0.042 0.263 3774 Planarity : 0.004 0.052 3504 Dihedral : 4.275 19.491 2619 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.67 % Allowed : 22.94 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2406 helix: 1.50 (0.26), residues: 459 sheet: 0.17 (0.18), residues: 753 loop : 0.22 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 504 TYR 0.050 0.002 TYR L 49 PHE 0.014 0.001 PHE D 63 TRP 0.011 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (21639) covalent geometry : angle 0.57565 / 0.29 (29364) SS BOND : bond 0.00220 / 0.16 ( 42) SS BOND : angle 0.70939 / 0.50 ( 84) hydrogen bonds : bond 0.03410 / 2.24 ( 771) hydrogen bonds : angle 4.97608 / 3.65 ( 2178) link_ALPHA1-2 : bond 0.00563 / 0.25 ( 3) link_ALPHA1-2 : angle 1.59971 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00442 / 0.30 ( 9) link_ALPHA1-3 : angle 1.37332 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00617 / 0.43 ( 9) link_ALPHA1-6 : angle 1.39127 / 0.95 ( 27) link_BETA1-4 : bond 0.00634 / 0.43 ( 75) link_BETA1-4 : angle 1.87744 / 1.33 ( 225) link_NAG-ASN : bond 0.00269 / 0.17 ( 63) link_NAG-ASN : angle 1.81705 / 1.33 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 257 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8521 (pt0) cc_final: 0.8320 (pm20) REVERT: A 657 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: C 356 ASN cc_start: 0.8860 (p0) cc_final: 0.8531 (p0) REVERT: C 416 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8160 (pp) REVERT: C 504 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6551 (mmt90) REVERT: G 114 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: G 356 ASN cc_start: 0.8800 (p0) cc_final: 0.8515 (p0) REVERT: G 504 ARG cc_start: 0.7081 (mmm160) cc_final: 0.6513 (mmt90) REVERT: I 356 ASN cc_start: 0.8800 (p0) cc_final: 0.8511 (p0) REVERT: I 504 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6503 (mmt90) REVERT: D 32 TYR cc_start: 0.7976 (m-80) cc_final: 0.7741 (m-10) REVERT: D 59 TYR cc_start: 0.7295 (m-80) cc_final: 0.7030 (m-80) REVERT: D 96 GLN cc_start: 0.7486 (mt0) cc_final: 0.7028 (mt0) REVERT: E 30 ASN cc_start: 0.6281 (t0) cc_final: 0.5731 (t0) REVERT: E 32 TYR cc_start: 0.6804 (m-80) cc_final: 0.5950 (m-80) REVERT: E 83 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7027 (mm) REVERT: H 28 LYS cc_start: 0.9258 (ptmm) cc_final: 0.9012 (pmtt) REVERT: H 31 ASP cc_start: 0.8745 (t0) cc_final: 0.8212 (t0) REVERT: H 32 TYR cc_start: 0.7969 (m-80) cc_final: 0.7410 (m-10) REVERT: H 64 ARG cc_start: 0.6385 (ttp-170) cc_final: 0.5984 (mtm-85) REVERT: H 94 ARG cc_start: 0.8486 (ptt180) cc_final: 0.8043 (ptt180) REVERT: H 95 LEU cc_start: 0.8422 (tp) cc_final: 0.8059 (tm) REVERT: H 96 GLN cc_start: 0.7777 (mt0) cc_final: 0.7544 (tt0) REVERT: L 32 TYR cc_start: 0.6643 (m-80) cc_final: 0.5721 (m-80) REVERT: L 48 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7849 (mm) REVERT: L 50 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8570 (tmmt) REVERT: L 75 ILE cc_start: 0.4592 (OUTLIER) cc_final: 0.4322 (mp) REVERT: L 83 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6983 (mm) REVERT: L 93 HIS cc_start: 0.8596 (m90) cc_final: 0.8226 (m-70) REVERT: J 31 ASP cc_start: 0.8872 (t0) cc_final: 0.8239 (t0) REVERT: J 32 TYR cc_start: 0.8176 (m-80) cc_final: 0.7941 (m-80) REVERT: J 96 GLN cc_start: 0.7763 (tt0) cc_final: 0.7462 (mt0) REVERT: K 30 ASN cc_start: 0.6620 (t0) cc_final: 0.6227 (t0) REVERT: K 50 LYS cc_start: 0.9066 (mmmm) cc_final: 0.8454 (tptp) REVERT: K 83 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6807 (mm) outliers start: 57 outliers final: 28 residues processed: 297 average time/residue: 0.5078 time to fit residues: 173.9728 Evaluate side-chains 283 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 229 optimal weight: 30.0000 chunk 196 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 103 GLN E 30 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.117112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063320 restraints weight = 40420.024| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.56 r_work: 0.2693 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21840 Z= 0.219 Angle : 0.656 9.774 29925 Z= 0.312 Chirality : 0.044 0.270 3774 Planarity : 0.004 0.045 3504 Dihedral : 4.396 19.390 2619 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.09 % Allowed : 22.80 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2406 helix: 1.46 (0.26), residues: 459 sheet: 0.14 (0.18), residues: 753 loop : 0.23 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 504 TYR 0.029 0.002 TYR J 27 PHE 0.014 0.001 PHE I 383 TRP 0.013 0.001 TRP I 96 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (21639) covalent geometry : angle 0.61609 / 0.30 (29364) SS BOND : bond 0.00289 / 0.21 ( 42) SS BOND : angle 0.80396 / 0.56 ( 84) hydrogen bonds : bond 0.03916 / 2.58 ( 771) hydrogen bonds : angle 5.03587 / 3.70 ( 2178) link_ALPHA1-2 : bond 0.00439 / 0.20 ( 3) link_ALPHA1-2 : angle 1.65011 / 1.00 ( 9) link_ALPHA1-3 : bond 0.00406 / 0.28 ( 9) link_ALPHA1-3 : angle 1.38253 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00613 / 0.42 ( 9) link_ALPHA1-6 : angle 1.36956 / 0.94 ( 27) link_BETA1-4 : bond 0.00630 / 0.42 ( 75) link_BETA1-4 : angle 1.91670 / 1.36 ( 225) link_NAG-ASN : bond 0.00460 / 0.29 ( 63) link_NAG-ASN : angle 1.95507 / 1.42 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 243 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: C 356 ASN cc_start: 0.8879 (p0) cc_final: 0.8542 (p0) REVERT: C 504 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6716 (mmt90) REVERT: G 114 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: G 356 ASN cc_start: 0.8830 (p0) cc_final: 0.8535 (p0) REVERT: G 504 ARG cc_start: 0.7236 (mmm160) cc_final: 0.6704 (mmt90) REVERT: I 356 ASN cc_start: 0.8841 (p0) cc_final: 0.8524 (p0) REVERT: I 504 ARG cc_start: 0.7219 (mmm160) cc_final: 0.6689 (mmt90) REVERT: D 23 LYS cc_start: 0.8896 (tppp) cc_final: 0.8618 (tppt) REVERT: D 28 LYS cc_start: 0.9220 (ptmm) cc_final: 0.8585 (pmtt) REVERT: D 31 ASP cc_start: 0.9028 (t0) cc_final: 0.8198 (p0) REVERT: D 32 TYR cc_start: 0.8104 (m-80) cc_final: 0.7436 (m-10) REVERT: D 59 TYR cc_start: 0.7272 (m-80) cc_final: 0.7023 (m-80) REVERT: D 96 GLN cc_start: 0.8004 (mt0) cc_final: 0.7568 (tp-100) REVERT: E 30 ASN cc_start: 0.6597 (t0) cc_final: 0.6056 (t0) REVERT: E 32 TYR cc_start: 0.6886 (m-80) cc_final: 0.5986 (m-80) REVERT: E 83 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7110 (mm) REVERT: H 28 LYS cc_start: 0.9235 (ptmm) cc_final: 0.8949 (pmtt) REVERT: H 31 ASP cc_start: 0.8766 (t0) cc_final: 0.8099 (t0) REVERT: H 32 TYR cc_start: 0.7926 (m-80) cc_final: 0.7330 (m-10) REVERT: H 64 ARG cc_start: 0.6407 (ttp-170) cc_final: 0.6010 (mtm-85) REVERT: H 96 GLN cc_start: 0.7799 (mt0) cc_final: 0.7527 (mt0) REVERT: L 32 TYR cc_start: 0.6662 (m-80) cc_final: 0.5703 (m-80) REVERT: L 48 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7577 (mm) REVERT: L 50 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8562 (tptp) REVERT: L 83 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6976 (mm) REVERT: J 31 ASP cc_start: 0.8661 (t0) cc_final: 0.8337 (t0) REVERT: J 95 LEU cc_start: 0.8523 (tp) cc_final: 0.8188 (tm) REVERT: J 96 GLN cc_start: 0.7785 (tt0) cc_final: 0.7331 (tt0) REVERT: K 30 ASN cc_start: 0.6659 (t0) cc_final: 0.6273 (t0) REVERT: K 50 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8507 (tptp) REVERT: K 83 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6835 (mm) outliers start: 66 outliers final: 34 residues processed: 286 average time/residue: 0.5511 time to fit residues: 180.8202 Evaluate side-chains 276 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 232 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 30.0000 chunk 165 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.117821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064303 restraints weight = 40537.530| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.61 r_work: 0.2723 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21840 Z= 0.142 Angle : 0.613 9.553 29925 Z= 0.292 Chirality : 0.042 0.263 3774 Planarity : 0.003 0.046 3504 Dihedral : 4.247 18.846 2619 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.81 % Allowed : 23.74 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2406 helix: 1.52 (0.26), residues: 459 sheet: 0.20 (0.18), residues: 747 loop : 0.29 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 504 TYR 0.030 0.002 TYR J 27 PHE 0.013 0.001 PHE C 53 TRP 0.011 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (21639) covalent geometry : angle 0.57409 / 0.28 (29364) SS BOND : bond 0.00232 / 0.17 ( 42) SS BOND : angle 0.70145 / 0.50 ( 84) hydrogen bonds : bond 0.03407 / 2.24 ( 771) hydrogen bonds : angle 4.89573 / 3.59 ( 2178) link_ALPHA1-2 : bond 0.00493 / 0.22 ( 3) link_ALPHA1-2 : angle 1.60608 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00417 / 0.29 ( 9) link_ALPHA1-3 : angle 1.39393 / 0.97 ( 27) link_ALPHA1-6 : bond 0.00585 / 0.40 ( 9) link_ALPHA1-6 : angle 1.38358 / 0.95 ( 27) link_BETA1-4 : bond 0.00614 / 0.41 ( 75) link_BETA1-4 : angle 1.80705 / 1.28 ( 225) link_NAG-ASN : bond 0.00264 / 0.17 ( 63) link_NAG-ASN : angle 1.85438 / 1.36 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8490 (pt0) cc_final: 0.8207 (pm20) REVERT: C 356 ASN cc_start: 0.8846 (p0) cc_final: 0.8519 (p0) REVERT: C 416 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8197 (pp) REVERT: C 504 ARG cc_start: 0.7245 (mmm160) cc_final: 0.6773 (mmt90) REVERT: F 621 GLU cc_start: 0.8645 (pt0) cc_final: 0.8357 (pm20) REVERT: G 114 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: G 356 ASN cc_start: 0.8794 (p0) cc_final: 0.8494 (p0) REVERT: G 504 ARG cc_start: 0.7231 (mmm160) cc_final: 0.6746 (mmt90) REVERT: I 100 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8608 (ptp) REVERT: I 356 ASN cc_start: 0.8797 (p0) cc_final: 0.8496 (p0) REVERT: I 504 ARG cc_start: 0.7237 (mmm160) cc_final: 0.6744 (mmt90) REVERT: D 28 LYS cc_start: 0.9270 (ptmm) cc_final: 0.8945 (pmtt) REVERT: D 31 ASP cc_start: 0.8805 (t0) cc_final: 0.7853 (OUTLIER) REVERT: D 32 TYR cc_start: 0.8193 (m-80) cc_final: 0.7622 (m-10) REVERT: D 59 TYR cc_start: 0.7261 (m-80) cc_final: 0.6992 (m-80) REVERT: D 96 GLN cc_start: 0.7918 (mt0) cc_final: 0.7423 (mt0) REVERT: E 30 ASN cc_start: 0.6634 (t0) cc_final: 0.6123 (t0) REVERT: E 32 TYR cc_start: 0.6815 (m-80) cc_final: 0.5845 (m-80) REVERT: E 48 ILE cc_start: 0.7993 (mm) cc_final: 0.7770 (mm) REVERT: E 83 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7059 (mm) REVERT: H 28 LYS cc_start: 0.9220 (ptmm) cc_final: 0.8962 (pmtt) REVERT: H 31 ASP cc_start: 0.8753 (t0) cc_final: 0.8141 (t0) REVERT: H 32 TYR cc_start: 0.7901 (m-80) cc_final: 0.7331 (m-10) REVERT: H 64 ARG cc_start: 0.6410 (ttp-170) cc_final: 0.6008 (mtm-85) REVERT: H 95 LEU cc_start: 0.8543 (tp) cc_final: 0.8194 (tm) REVERT: H 96 GLN cc_start: 0.7799 (mt0) cc_final: 0.7540 (mt0) REVERT: L 32 TYR cc_start: 0.6629 (m-80) cc_final: 0.5699 (m-80) REVERT: L 49 TYR cc_start: 0.7890 (p90) cc_final: 0.7584 (p90) REVERT: L 50 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8501 (tptp) REVERT: L 83 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7013 (mm) REVERT: L 93 HIS cc_start: 0.8502 (m90) cc_final: 0.8114 (m-70) REVERT: J 28 LYS cc_start: 0.9255 (ptmm) cc_final: 0.9013 (pmtt) REVERT: J 31 ASP cc_start: 0.8893 (t0) cc_final: 0.8377 (t0) REVERT: J 32 TYR cc_start: 0.8035 (m-80) cc_final: 0.7702 (m-10) REVERT: J 96 GLN cc_start: 0.7902 (tt0) cc_final: 0.7343 (tp-100) REVERT: K 30 ASN cc_start: 0.6726 (t0) cc_final: 0.6291 (t0) REVERT: K 50 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8580 (tptp) REVERT: K 83 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6881 (mm) outliers start: 60 outliers final: 40 residues processed: 291 average time/residue: 0.5421 time to fit residues: 180.7518 Evaluate side-chains 285 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 158 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 411 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.117827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.064417 restraints weight = 40455.742| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.60 r_work: 0.2725 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21840 Z= 0.138 Angle : 0.615 9.635 29925 Z= 0.293 Chirality : 0.042 0.267 3774 Planarity : 0.004 0.048 3504 Dihedral : 4.216 18.826 2619 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.48 % Allowed : 24.02 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2406 helix: 1.58 (0.26), residues: 459 sheet: 0.23 (0.18), residues: 744 loop : 0.31 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 151 TYR 0.035 0.002 TYR K 49 PHE 0.013 0.001 PHE K 89 TRP 0.012 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (21639) covalent geometry : angle 0.57851 / 0.29 (29364) SS BOND : bond 0.00241 / 0.18 ( 42) SS BOND : angle 0.69396 / 0.48 ( 84) hydrogen bonds : bond 0.03357 / 2.21 ( 771) hydrogen bonds : angle 4.85140 / 3.57 ( 2178) link_ALPHA1-2 : bond 0.00485 / 0.22 ( 3) link_ALPHA1-2 : angle 1.59830 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00417 / 0.29 ( 9) link_ALPHA1-3 : angle 1.38411 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00573 / 0.40 ( 9) link_ALPHA1-6 : angle 1.38206 / 0.95 ( 27) link_BETA1-4 : bond 0.00620 / 0.41 ( 75) link_BETA1-4 : angle 1.78027 / 1.27 ( 225) link_NAG-ASN : bond 0.00280 / 0.18 ( 63) link_NAG-ASN : angle 1.80306 / 1.32 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8497 (pt0) cc_final: 0.8202 (pm20) REVERT: C 356 ASN cc_start: 0.8840 (p0) cc_final: 0.8522 (p0) REVERT: C 416 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8180 (pp) REVERT: C 504 ARG cc_start: 0.7251 (mmm160) cc_final: 0.6802 (mmt90) REVERT: F 621 GLU cc_start: 0.8648 (pt0) cc_final: 0.8306 (pm20) REVERT: G 114 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: G 356 ASN cc_start: 0.8789 (p0) cc_final: 0.8496 (p0) REVERT: G 504 ARG cc_start: 0.7235 (mmm160) cc_final: 0.6782 (mmt90) REVERT: I 100 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (ptp) REVERT: I 356 ASN cc_start: 0.8771 (p0) cc_final: 0.8470 (p0) REVERT: I 504 ARG cc_start: 0.7295 (mmm160) cc_final: 0.6789 (mmt90) REVERT: D 28 LYS cc_start: 0.9241 (ptmm) cc_final: 0.8924 (pmtt) REVERT: D 31 ASP cc_start: 0.8757 (t0) cc_final: 0.7543 (t70) REVERT: D 32 TYR cc_start: 0.8216 (m-80) cc_final: 0.7221 (m-10) REVERT: D 59 TYR cc_start: 0.7237 (m-80) cc_final: 0.6971 (m-80) REVERT: D 95 LEU cc_start: 0.8559 (tp) cc_final: 0.8209 (tm) REVERT: D 96 GLN cc_start: 0.7957 (mt0) cc_final: 0.7124 (tp40) REVERT: E 30 ASN cc_start: 0.6746 (t0) cc_final: 0.6270 (t0) REVERT: E 32 TYR cc_start: 0.6801 (m-80) cc_final: 0.5794 (m-80) REVERT: E 35 TRP cc_start: 0.5554 (m100) cc_final: 0.5210 (m-90) REVERT: E 83 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7111 (mm) REVERT: H 28 LYS cc_start: 0.9206 (ptmm) cc_final: 0.8815 (tppt) REVERT: H 31 ASP cc_start: 0.8764 (t0) cc_final: 0.8361 (p0) REVERT: H 64 ARG cc_start: 0.6395 (ttp-170) cc_final: 0.5995 (mtm-85) REVERT: H 95 LEU cc_start: 0.8498 (tp) cc_final: 0.8191 (tm) REVERT: H 96 GLN cc_start: 0.7840 (mt0) cc_final: 0.7607 (tp40) REVERT: L 32 TYR cc_start: 0.6518 (m-80) cc_final: 0.5551 (m-80) REVERT: L 49 TYR cc_start: 0.7826 (p90) cc_final: 0.7563 (p90) REVERT: L 50 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8486 (tptp) REVERT: L 83 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7036 (mm) REVERT: L 93 HIS cc_start: 0.8507 (m90) cc_final: 0.8104 (m-70) REVERT: J 28 LYS cc_start: 0.9224 (ptmm) cc_final: 0.8969 (pmtt) REVERT: J 31 ASP cc_start: 0.8885 (t0) cc_final: 0.8173 (t0) REVERT: J 32 TYR cc_start: 0.8019 (m-80) cc_final: 0.7666 (m-10) REVERT: J 95 LEU cc_start: 0.8483 (tp) cc_final: 0.8145 (tm) REVERT: J 96 GLN cc_start: 0.7899 (tt0) cc_final: 0.7430 (mt0) REVERT: K 30 ASN cc_start: 0.6736 (t0) cc_final: 0.6368 (t0) REVERT: K 50 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8590 (tptp) REVERT: K 83 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6947 (mm) outliers start: 53 outliers final: 38 residues processed: 285 average time/residue: 0.5310 time to fit residues: 173.8513 Evaluate side-chains 286 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 102 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 138 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.117877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064708 restraints weight = 40473.078| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.58 r_work: 0.2733 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21840 Z= 0.130 Angle : 0.617 9.615 29925 Z= 0.294 Chirality : 0.042 0.265 3774 Planarity : 0.004 0.055 3504 Dihedral : 4.194 18.724 2619 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.34 % Allowed : 24.58 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2406 helix: 1.59 (0.26), residues: 459 sheet: 0.23 (0.19), residues: 744 loop : 0.31 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 151 TYR 0.029 0.001 TYR J 27 PHE 0.014 0.001 PHE J 63 TRP 0.012 0.001 TRP I 96 HIS 0.002 0.001 HIS I 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (21639) covalent geometry : angle 0.58127 / 0.29 (29364) SS BOND : bond 0.00236 / 0.17 ( 42) SS BOND : angle 0.68889 / 0.48 ( 84) hydrogen bonds : bond 0.03281 / 2.16 ( 771) hydrogen bonds : angle 4.82209 / 3.55 ( 2178) link_ALPHA1-2 : bond 0.00491 / 0.22 ( 3) link_ALPHA1-2 : angle 1.59027 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00421 / 0.29 ( 9) link_ALPHA1-3 : angle 1.38835 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00573 / 0.40 ( 9) link_ALPHA1-6 : angle 1.38196 / 0.95 ( 27) link_BETA1-4 : bond 0.00608 / 0.40 ( 75) link_BETA1-4 : angle 1.75678 / 1.25 ( 225) link_NAG-ASN : bond 0.00249 / 0.16 ( 63) link_NAG-ASN : angle 1.78449 / 1.31 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8535 (pt0) cc_final: 0.8246 (pm20) REVERT: C 356 ASN cc_start: 0.8852 (p0) cc_final: 0.8542 (p0) REVERT: C 416 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8142 (pp) REVERT: C 504 ARG cc_start: 0.7280 (mmm160) cc_final: 0.6830 (mmt90) REVERT: F 621 GLU cc_start: 0.8653 (pt0) cc_final: 0.8315 (pm20) REVERT: G 114 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: G 356 ASN cc_start: 0.8777 (p0) cc_final: 0.8468 (p0) REVERT: G 504 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6797 (mmt90) REVERT: I 100 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8577 (ptp) REVERT: I 232 LYS cc_start: 0.8880 (tppt) cc_final: 0.8523 (mmtp) REVERT: I 356 ASN cc_start: 0.8752 (p0) cc_final: 0.8456 (p0) REVERT: I 504 ARG cc_start: 0.7295 (mmm160) cc_final: 0.6824 (mmt90) REVERT: D 23 LYS cc_start: 0.8831 (tppp) cc_final: 0.8556 (tppt) REVERT: D 28 LYS cc_start: 0.9245 (ptmm) cc_final: 0.8920 (pmtt) REVERT: D 31 ASP cc_start: 0.8766 (t0) cc_final: 0.7618 (t70) REVERT: D 32 TYR cc_start: 0.8249 (m-80) cc_final: 0.7188 (m-80) REVERT: D 59 TYR cc_start: 0.7262 (m-80) cc_final: 0.7051 (m-80) REVERT: D 95 LEU cc_start: 0.8513 (tp) cc_final: 0.8181 (tm) REVERT: D 96 GLN cc_start: 0.8025 (mt0) cc_final: 0.7126 (tp40) REVERT: E 30 ASN cc_start: 0.6795 (t0) cc_final: 0.6284 (t0) REVERT: E 32 TYR cc_start: 0.6729 (m-80) cc_final: 0.5785 (m-80) REVERT: E 35 TRP cc_start: 0.5446 (m100) cc_final: 0.5054 (m-90) REVERT: E 83 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7118 (mm) REVERT: H 23 LYS cc_start: 0.8903 (tppp) cc_final: 0.8632 (tppt) REVERT: H 31 ASP cc_start: 0.8762 (t0) cc_final: 0.8315 (t0) REVERT: H 32 TYR cc_start: 0.7925 (m-80) cc_final: 0.7503 (m-10) REVERT: H 64 ARG cc_start: 0.6410 (ttp-170) cc_final: 0.6011 (mtm-85) REVERT: H 95 LEU cc_start: 0.8484 (tp) cc_final: 0.8157 (tm) REVERT: H 96 GLN cc_start: 0.7850 (mt0) cc_final: 0.7443 (mt0) REVERT: L 32 TYR cc_start: 0.6460 (m-80) cc_final: 0.5568 (m-80) REVERT: L 49 TYR cc_start: 0.7832 (p90) cc_final: 0.7584 (p90) REVERT: L 50 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8477 (tptp) REVERT: L 83 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7009 (mm) REVERT: L 93 HIS cc_start: 0.8520 (m90) cc_final: 0.8141 (m-70) REVERT: J 28 LYS cc_start: 0.9208 (ptmm) cc_final: 0.8943 (pmtt) REVERT: J 31 ASP cc_start: 0.8881 (t0) cc_final: 0.8101 (t0) REVERT: J 32 TYR cc_start: 0.8012 (m-80) cc_final: 0.7613 (m-10) REVERT: J 95 LEU cc_start: 0.8513 (tp) cc_final: 0.8176 (tm) REVERT: J 96 GLN cc_start: 0.7940 (tt0) cc_final: 0.7446 (mt0) REVERT: J 103 TRP cc_start: 0.7974 (m100) cc_final: 0.7359 (m100) REVERT: K 30 ASN cc_start: 0.6804 (t0) cc_final: 0.6407 (t0) REVERT: K 50 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8530 (tptp) REVERT: K 83 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6960 (mm) outliers start: 50 outliers final: 35 residues processed: 282 average time/residue: 0.5094 time to fit residues: 164.8534 Evaluate side-chains 282 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.117776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064608 restraints weight = 40536.787| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.58 r_work: 0.2727 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21840 Z= 0.139 Angle : 0.631 9.618 29925 Z= 0.301 Chirality : 0.042 0.265 3774 Planarity : 0.004 0.063 3504 Dihedral : 4.223 18.793 2619 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.34 % Allowed : 24.49 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2406 helix: 1.59 (0.26), residues: 459 sheet: 0.26 (0.19), residues: 738 loop : 0.28 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 151 TYR 0.034 0.002 TYR E 49 PHE 0.013 0.001 PHE E 89 TRP 0.012 0.001 TRP I 96 HIS 0.002 0.001 HIS I 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21639) covalent geometry : angle 0.59706 / 0.29 (29364) SS BOND : bond 0.00249 / 0.19 ( 42) SS BOND : angle 0.75515 / 0.53 ( 84) hydrogen bonds : bond 0.03319 / 2.18 ( 771) hydrogen bonds : angle 4.81963 / 3.55 ( 2178) link_ALPHA1-2 : bond 0.00482 / 0.21 ( 3) link_ALPHA1-2 : angle 1.58280 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00414 / 0.28 ( 9) link_ALPHA1-3 : angle 1.38529 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00571 / 0.39 ( 9) link_ALPHA1-6 : angle 1.37973 / 0.95 ( 27) link_BETA1-4 : bond 0.00607 / 0.40 ( 75) link_BETA1-4 : angle 1.74111 / 1.24 ( 225) link_NAG-ASN : bond 0.00264 / 0.17 ( 63) link_NAG-ASN : angle 1.77396 / 1.29 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8850 (p0) cc_final: 0.8548 (p0) REVERT: C 416 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8127 (pp) REVERT: C 504 ARG cc_start: 0.7304 (mmm160) cc_final: 0.6865 (mmt90) REVERT: G 114 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: G 356 ASN cc_start: 0.8774 (p0) cc_final: 0.8478 (p0) REVERT: G 504 ARG cc_start: 0.7267 (mmm160) cc_final: 0.6824 (mmt90) REVERT: I 100 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8582 (ptp) REVERT: I 232 LYS cc_start: 0.8868 (tppt) cc_final: 0.8517 (mmtp) REVERT: I 356 ASN cc_start: 0.8762 (p0) cc_final: 0.8478 (p0) REVERT: I 504 ARG cc_start: 0.7305 (mmm160) cc_final: 0.6832 (mmt90) REVERT: D 23 LYS cc_start: 0.8810 (tppp) cc_final: 0.8570 (tppt) REVERT: D 31 ASP cc_start: 0.8753 (t0) cc_final: 0.8091 (t70) REVERT: D 32 TYR cc_start: 0.8234 (m-80) cc_final: 0.7608 (m-80) REVERT: D 59 TYR cc_start: 0.7233 (m-80) cc_final: 0.7027 (m-80) REVERT: D 96 GLN cc_start: 0.7977 (mt0) cc_final: 0.7060 (mm-40) REVERT: E 30 ASN cc_start: 0.6720 (t0) cc_final: 0.6273 (t0) REVERT: E 32 TYR cc_start: 0.6653 (m-80) cc_final: 0.5777 (m-80) REVERT: E 35 TRP cc_start: 0.5347 (m100) cc_final: 0.5040 (m-90) REVERT: E 83 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7107 (mm) REVERT: H 23 LYS cc_start: 0.8887 (tppp) cc_final: 0.8644 (tppt) REVERT: H 31 ASP cc_start: 0.8722 (t0) cc_final: 0.8272 (t0) REVERT: H 32 TYR cc_start: 0.7899 (m-80) cc_final: 0.7438 (m-10) REVERT: H 64 ARG cc_start: 0.6382 (ttp-170) cc_final: 0.5984 (mtm-85) REVERT: H 95 LEU cc_start: 0.8453 (tp) cc_final: 0.8142 (tm) REVERT: H 96 GLN cc_start: 0.7842 (mt0) cc_final: 0.7449 (mt0) REVERT: L 30 ASN cc_start: 0.6206 (t0) cc_final: 0.5783 (t0) REVERT: L 32 TYR cc_start: 0.6467 (m-80) cc_final: 0.5414 (m-80) REVERT: L 49 TYR cc_start: 0.7830 (p90) cc_final: 0.7621 (p90) REVERT: L 50 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8479 (tptp) REVERT: L 83 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7035 (mm) REVERT: L 93 HIS cc_start: 0.8496 (m90) cc_final: 0.8121 (m-70) REVERT: J 23 LYS cc_start: 0.8837 (tppp) cc_final: 0.8588 (tppt) REVERT: J 28 LYS cc_start: 0.9131 (ptmm) cc_final: 0.8899 (pmtt) REVERT: J 31 ASP cc_start: 0.8877 (t0) cc_final: 0.8068 (t0) REVERT: J 32 TYR cc_start: 0.7982 (m-80) cc_final: 0.7554 (m-10) REVERT: J 95 LEU cc_start: 0.8484 (tp) cc_final: 0.8153 (tm) REVERT: J 96 GLN cc_start: 0.7935 (tt0) cc_final: 0.7440 (mt0) REVERT: J 103 TRP cc_start: 0.7973 (m100) cc_final: 0.7373 (m100) REVERT: K 30 ASN cc_start: 0.6942 (t0) cc_final: 0.6522 (t0) REVERT: K 50 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8475 (tptp) REVERT: K 83 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6980 (mm) outliers start: 50 outliers final: 38 residues processed: 287 average time/residue: 0.5157 time to fit residues: 169.9460 Evaluate side-chains 288 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 231 optimal weight: 40.0000 chunk 138 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 28 optimal weight: 4.9990 chunk 166 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 348 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.118204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065187 restraints weight = 40485.020| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.61 r_work: 0.2746 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21840 Z= 0.121 Angle : 0.629 9.595 29925 Z= 0.301 Chirality : 0.042 0.264 3774 Planarity : 0.004 0.074 3504 Dihedral : 4.186 18.514 2619 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.11 % Allowed : 24.67 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2406 helix: 1.61 (0.26), residues: 459 sheet: 0.29 (0.19), residues: 738 loop : 0.27 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 151 TYR 0.031 0.002 TYR J 27 PHE 0.014 0.001 PHE K 89 TRP 0.013 0.001 TRP I 96 HIS 0.001 0.000 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21639) covalent geometry : angle 0.59533 / 0.29 (29364) SS BOND : bond 0.00214 / 0.16 ( 42) SS BOND : angle 0.79886 / 0.60 ( 84) hydrogen bonds : bond 0.03152 / 2.07 ( 771) hydrogen bonds : angle 4.79751 / 3.53 ( 2178) link_ALPHA1-2 : bond 0.00497 / 0.22 ( 3) link_ALPHA1-2 : angle 1.56955 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00468 / 0.33 ( 9) link_ALPHA1-3 : angle 1.40274 / 0.97 ( 27) link_ALPHA1-6 : bond 0.00575 / 0.40 ( 9) link_ALPHA1-6 : angle 1.38689 / 0.95 ( 27) link_BETA1-4 : bond 0.00603 / 0.40 ( 75) link_BETA1-4 : angle 1.71570 / 1.22 ( 225) link_NAG-ASN : bond 0.00216 / 0.14 ( 63) link_NAG-ASN : angle 1.75494 / 1.29 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8087.18 seconds wall clock time: 138 minutes 27.34 seconds (8307.34 seconds total)