Starting phenix.real_space_refine on Sat Jul 4 12:36:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.map" model { file = "/net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4m_29725/07_2026/8g4m_29725.cif" } resolution = 2.95 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= 0.013 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 135 5.16 5 C 12837 2.51 5 N 3409 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 20584 Number of models: 1 Model: "" Number of chains: 61 Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1042 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "G" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "J" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" 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: "o" 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.54, per 1000 atoms: 0.22 Number of scatterers: 20584 At special positions: 0 Unit cell: (130.31, 132.8, 144.42, 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 135 16.00 O 4203 8.00 N 3409 7.00 C 12837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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 C 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 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 G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 I 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100D" 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 H 99 " - pdb=" SG CYS H 100D" 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 J 99 " - pdb=" SG CYS J 100D" 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 t 4 " - " MAN t 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 6 " " BMA a 3 " - " MAN a 5 " " BMA o 3 " - " MAN o 5 " " BMA t 3 " - " MAN t 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN I 392 " " NAG 1 1 " - " ASN I 448 " " NAG 2 1 " - " ASN I 160 " " NAG A 701 " - " ASN A 637 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 234 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG I 601 " - " ASN I 339 " " NAG I 602 " - " ASN I 355 " " NAG M 1 " - " ASN C 88 " " NAG N 1 " - " ASN C 133 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 197 " " 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 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN G 88 " " NAG b 1 " - " ASN G 133 " " NAG c 1 " - " ASN G 156 " " NAG d 1 " - " ASN G 197 " " 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 392 " " NAG m 1 " - " ASN G 448 " " NAG n 1 " - " ASN G 160 " " NAG o 1 " - " ASN I 88 " " NAG p 1 " - " ASN I 133 " " NAG q 1 " - " ASN I 156 " " NAG r 1 " - " ASN I 197 " " NAG s 1 " - " ASN I 234 " " NAG t 1 " - " ASN I 262 " " NAG u 1 " - " ASN I 276 " " NAG v 1 " - " ASN I 295 " " NAG w 1 " - " ASN I 301 " " NAG x 1 " - " ASN I 332 " " NAG y 1 " - " ASN I 363 " " NAG z 1 " - " ASN I 386 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 707.8 milliseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 45 sheets defined 20.5% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.882A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.542A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.616A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.675A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.771A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.532A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.560A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.592A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.839A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.618A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.736A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.713A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.577A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.632A pdb=" N ALA I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.227A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 removed outlier: 3.931A 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: 4.030A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.917A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 4.164A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.471A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.744A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.755A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.513A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.932A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.690A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.248A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.601A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.640A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 203 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 259 through 261 removed outlier: 6.452A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.586A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.345A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.657A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.263A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.470A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.617A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.544A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.633A 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 Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.656A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.171A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.508A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.430A 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: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.561A 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 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.041A pdb=" N ARG D 38 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.279A pdb=" N TYR D 102 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.070A pdb=" N GLU E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.097A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.438A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.342A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.554A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.591A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.113A pdb=" N ARG J 38 " --> pdb=" O TYR J 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.059A pdb=" N TYR J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.141A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2046 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: 3.90 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6415 1.34 - 1.46: 5264 1.46 - 1.58: 9118 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 20977 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" N GLU J 1 " pdb=" CA GLU J 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" C1 NAG p 2 " pdb=" O5 NAG p 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 20972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 27952 2.19 - 4.39: 435 4.39 - 6.58: 71 6.58 - 8.77: 0 8.77 - 10.97: 1 Bond angle restraints: 28459 Sorted by residual: angle pdb=" C2 NAG b 2 " pdb=" N2 NAG b 2 " pdb=" C7 NAG b 2 " ideal model delta sigma weight residual 124.56 135.53 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA ILE B 635 " pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " ideal model delta sigma weight residual 110.40 115.22 -4.82 1.70e+00 3.46e-01 8.03e+00 angle pdb=" N GLY I 389 " pdb=" CA GLY I 389 " pdb=" C GLY I 389 " ideal model delta sigma weight residual 114.66 111.25 3.41 1.24e+00 6.50e-01 7.56e+00 angle pdb=" C GLY K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.43e+00 angle pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " pdb=" CD1 ILE B 635 " ideal model delta sigma weight residual 113.80 119.50 -5.70 2.10e+00 2.27e-01 7.38e+00 ... (remaining 28454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10064 17.90 - 35.81: 1125 35.81 - 53.71: 344 53.71 - 71.61: 83 71.61 - 89.52: 25 Dihedral angle restraints: 11641 sinusoidal: 4648 harmonic: 6993 Sorted by residual: dihedral pdb=" CB CYS I 201 " pdb=" SG CYS I 201 " pdb=" SG CYS I 433 " pdb=" CB CYS I 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.45 62.45 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS D 99 " pdb=" SG CYS D 99 " pdb=" SG CYS D 100D" pdb=" CB CYS D 100D" ideal model delta sinusoidal sigma weight residual 93.00 153.67 -60.67 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -139.44 53.44 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 11638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3030 0.059 - 0.119: 419 0.119 - 0.178: 66 0.178 - 0.238: 6 0.238 - 0.297: 8 Chirality restraints: 3529 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3526 not shown) Planarity restraints: 3521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 18 " -0.176 9.50e-02 1.11e+02 7.93e-02 4.15e+00 pdb=" NE ARG K 18 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG K 18 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG K 18 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG K 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 55 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" CG ASP J 55 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP J 55 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP J 55 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 635 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C ILE B 635 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE B 635 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 636 " 0.006 2.00e-02 2.50e+03 ... (remaining 3518 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 537 2.69 - 3.24: 19246 3.24 - 3.79: 31779 3.79 - 4.35: 44438 4.35 - 4.90: 74271 Nonbonded interactions: 170271 Sorted by model distance: nonbonded pdb=" N GLU K 81 " pdb=" OE1 GLU K 81 " model vdw 2.132 3.120 nonbonded pdb=" N GLU E 81 " pdb=" OE1 GLU E 81 " model vdw 2.136 3.120 nonbonded pdb=" OE1 GLN I 258 " pdb=" OG1 THR I 387 " model vdw 2.140 3.040 nonbonded pdb=" O SER G 460 " pdb=" OG1 THR G 461 " model vdw 2.161 3.040 nonbonded pdb=" O SER I 460 " pdb=" OG1 THR I 461 " model vdw 2.188 3.040 ... (remaining 170266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'A' and resid 514 through 701) selection = chain 'B' selection = (chain 'F' and resid 514 through 701) } ncs_group { reference = (chain 'C' and resid 31 through 602) selection = (chain 'G' and resid 31 through 602) 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 'a' selection = chain 'e' selection = chain 'o' } ncs_group { reference = chain 'Q' selection = chain 't' } 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: 7.020 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.540 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 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 : 0.004 0.040 21141 Z= 0.216 Angle : 0.659 10.968 28906 Z= 0.282 Chirality : 0.047 0.297 3529 Planarity : 0.003 0.079 3466 Dihedral : 16.845 89.516 7014 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.43 % Allowed : 21.18 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.60 (0.18), residues: 2384 helix: 1.74 (0.29), residues: 412 sheet: 0.15 (0.19), residues: 771 loop : 0.22 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 18 TYR 0.012 0.001 TYR D 100E PHE 0.007 0.001 PHE D 100G TRP 0.007 0.001 TRP G 96 HIS 0.003 0.000 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (20977) covalent geometry : angle 0.63825 / 0.28 (28459) SS BOND : bond 0.00149 / 0.10 ( 45) SS BOND : angle 0.42175 / 0.27 ( 90) hydrogen bonds : bond 0.20304 / 13.56 ( 744) hydrogen bonds : angle 8.34713 / 5.86 ( 2046) link_ALPHA1-2 : bond 0.00595 / 0.21 ( 3) link_ALPHA1-2 : angle 2.70991 / 1.45 ( 9) link_ALPHA1-3 : bond 0.00286 / 0.17 ( 6) link_ALPHA1-3 : angle 1.79232 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00391 / 0.19 ( 5) link_ALPHA1-6 : angle 1.75237 / 0.99 ( 15) link_BETA1-4 : bond 0.00357 / 0.19 ( 50) link_BETA1-4 : angle 1.50162 / 1.02 ( 150) link_NAG-ASN : bond 0.00225 / 0.14 ( 55) link_NAG-ASN : angle 1.63079 / 1.11 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.8458 (tpp) cc_final: 0.8173 (mpp) REVERT: A 601 LYS cc_start: 0.8922 (mttm) cc_final: 0.8625 (mttp) REVERT: G 475 MET cc_start: 0.8732 (mmm) cc_final: 0.7608 (mpp) REVERT: B 655 LYS cc_start: 0.8419 (tptm) cc_final: 0.8210 (tptp) REVERT: F 599 SER cc_start: 0.9376 (t) cc_final: 0.9056 (m) REVERT: D 3 GLN cc_start: 0.8140 (mm110) cc_final: 0.7565 (mp10) REVERT: D 13 GLN cc_start: 0.8777 (mp10) cc_final: 0.8514 (tp40) REVERT: D 72 ASP cc_start: 0.8104 (t0) cc_final: 0.7336 (t0) REVERT: D 83 ARG cc_start: 0.9160 (mtm-85) cc_final: 0.8905 (ptp-170) REVERT: D 100 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8084 (mtp85) REVERT: D 107 THR cc_start: 0.9026 (t) cc_final: 0.8788 (p) REVERT: E 5 THR cc_start: 0.9172 (m) cc_final: 0.8960 (p) REVERT: H 38 ARG cc_start: 0.8828 (ptt180) cc_final: 0.8575 (ptt-90) REVERT: H 72 ASP cc_start: 0.8214 (t0) cc_final: 0.7890 (t0) REVERT: H 85 GLU cc_start: 0.8953 (pm20) cc_final: 0.8688 (pm20) REVERT: H 89 VAL cc_start: 0.8596 (t) cc_final: 0.8260 (p) REVERT: H 107 THR cc_start: 0.8795 (t) cc_final: 0.8451 (p) REVERT: L 24 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: L 70 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8272 (mm-30) REVERT: J 13 GLN cc_start: 0.8563 (mm110) cc_final: 0.8267 (mm110) REVERT: J 43 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8439 (mppt) REVERT: J 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7683 (t70) REVERT: K 79 GLN cc_start: 0.8369 (mt0) cc_final: 0.8148 (mt0) outliers start: 51 outliers final: 39 residues processed: 306 average time/residue: 0.6453 time to fit residues: 221.4610 Evaluate side-chains 257 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 388 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 80 ASN C 411 ASN A 651 ASN G 80 ASN I 67 ASN F 656 ASN D 3 GLN H 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.052400 restraints weight = 48334.721| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.38 r_work: 0.2540 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21141 Z= 0.169 Angle : 0.604 12.413 28906 Z= 0.293 Chirality : 0.044 0.375 3529 Planarity : 0.003 0.035 3466 Dihedral : 5.148 59.999 2663 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.86 % Allowed : 20.47 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.72 (0.18), residues: 2384 helix: 2.40 (0.29), residues: 384 sheet: 0.09 (0.19), residues: 759 loop : 0.23 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 18 TYR 0.017 0.001 TYR J 100E PHE 0.011 0.001 PHE F 519 TRP 0.010 0.001 TRP G 96 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (20977) covalent geometry : angle 0.58223 / 0.29 (28459) SS BOND : bond 0.00254 / 0.16 ( 45) SS BOND : angle 0.74931 / 0.52 ( 90) hydrogen bonds : bond 0.04597 / 3.05 ( 744) hydrogen bonds : angle 5.82280 / 4.08 ( 2046) link_ALPHA1-2 : bond 0.01251 / 0.46 ( 3) link_ALPHA1-2 : angle 2.16642 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00505 / 0.29 ( 6) link_ALPHA1-3 : angle 1.42424 / 0.85 ( 18) link_ALPHA1-6 : bond 0.00364 / 0.19 ( 5) link_ALPHA1-6 : angle 1.56644 / 0.86 ( 15) link_BETA1-4 : bond 0.00440 / 0.28 ( 50) link_BETA1-4 : angle 1.28491 / 0.86 ( 150) link_NAG-ASN : bond 0.00359 / 0.21 ( 55) link_NAG-ASN : angle 1.73122 / 1.17 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: C 475 MET cc_start: 0.8570 (tpp) cc_final: 0.8368 (mpp) REVERT: A 601 LYS cc_start: 0.9133 (mttm) cc_final: 0.8818 (mtmm) REVERT: G 475 MET cc_start: 0.8800 (mmm) cc_final: 0.8009 (mpp) REVERT: B 632 ASP cc_start: 0.9122 (t0) cc_final: 0.8827 (t0) REVERT: B 655 LYS cc_start: 0.8809 (tptm) cc_final: 0.8508 (tptm) REVERT: F 599 SER cc_start: 0.9494 (t) cc_final: 0.9233 (p) REVERT: F 621 GLU cc_start: 0.9035 (tt0) cc_final: 0.8581 (pt0) REVERT: F 655 LYS cc_start: 0.7915 (tptt) cc_final: 0.7631 (ttmt) REVERT: D 13 GLN cc_start: 0.8839 (mp10) cc_final: 0.8375 (mm-40) REVERT: D 34 MET cc_start: 0.9127 (mmt) cc_final: 0.8883 (tpp) REVERT: D 72 ASP cc_start: 0.8268 (t0) cc_final: 0.7579 (t0) REVERT: D 89 VAL cc_start: 0.9032 (t) cc_final: 0.8757 (p) REVERT: D 100 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8142 (mtp85) REVERT: E 11 LEU cc_start: 0.7561 (tt) cc_final: 0.7354 (tt) REVERT: E 45 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8675 (ttp80) REVERT: H 85 GLU cc_start: 0.9178 (pm20) cc_final: 0.8894 (pm20) REVERT: L 24 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7962 (ttp80) REVERT: J 13 GLN cc_start: 0.8705 (mm110) cc_final: 0.8441 (mm110) REVERT: J 72 ASP cc_start: 0.8425 (t0) cc_final: 0.7945 (t70) REVERT: K 17 GLU cc_start: 0.8845 (pt0) cc_final: 0.8622 (pm20) REVERT: K 79 GLN cc_start: 0.8724 (mt0) cc_final: 0.8213 (mt0) outliers start: 60 outliers final: 23 residues processed: 292 average time/residue: 0.6754 time to fit residues: 220.5339 Evaluate side-chains 245 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 138 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN C 411 ASN G 80 ASN I 67 ASN F 656 ASN D 3 GLN H 13 GLN H 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.052875 restraints weight = 48270.164| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.46 r_work: 0.2550 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21141 Z= 0.131 Angle : 0.562 10.657 28906 Z= 0.270 Chirality : 0.043 0.376 3529 Planarity : 0.003 0.039 3466 Dihedral : 4.407 44.144 2632 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.43 % Allowed : 21.47 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.86 (0.18), residues: 2384 helix: 3.02 (0.29), residues: 358 sheet: 0.15 (0.19), residues: 756 loop : 0.22 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 18 TYR 0.016 0.001 TYR J 100E PHE 0.010 0.001 PHE G 383 TRP 0.010 0.001 TRP G 96 HIS 0.003 0.000 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (20977) covalent geometry : angle 0.53944 / 0.27 (28459) SS BOND : bond 0.00206 / 0.13 ( 45) SS BOND : angle 0.58802 / 0.42 ( 90) hydrogen bonds : bond 0.03930 / 2.61 ( 744) hydrogen bonds : angle 5.30353 / 3.72 ( 2046) link_ALPHA1-2 : bond 0.00919 / 0.37 ( 3) link_ALPHA1-2 : angle 2.13966 / 1.15 ( 9) link_ALPHA1-3 : bond 0.00624 / 0.35 ( 6) link_ALPHA1-3 : angle 1.30403 / 0.77 ( 18) link_ALPHA1-6 : bond 0.00426 / 0.23 ( 5) link_ALPHA1-6 : angle 1.46532 / 0.80 ( 15) link_BETA1-4 : bond 0.00347 / 0.21 ( 50) link_BETA1-4 : angle 1.26740 / 0.83 ( 150) link_NAG-ASN : bond 0.00299 / 0.17 ( 55) link_NAG-ASN : angle 1.67981 / 1.12 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 233 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: C 475 MET cc_start: 0.8529 (tpp) cc_final: 0.8315 (mpp) REVERT: A 601 LYS cc_start: 0.9149 (mttm) cc_final: 0.8839 (mtmm) REVERT: G 475 MET cc_start: 0.8754 (mmm) cc_final: 0.7989 (mpp) REVERT: B 632 ASP cc_start: 0.9152 (t0) cc_final: 0.8885 (t0) REVERT: B 655 LYS cc_start: 0.8744 (tptm) cc_final: 0.8457 (tptm) REVERT: F 599 SER cc_start: 0.9483 (t) cc_final: 0.9242 (p) REVERT: F 621 GLU cc_start: 0.9015 (tt0) cc_final: 0.8780 (pt0) REVERT: F 655 LYS cc_start: 0.7928 (tptt) cc_final: 0.7609 (ttpt) REVERT: D 3 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8392 (mm-40) REVERT: D 13 GLN cc_start: 0.8853 (mp10) cc_final: 0.8358 (mm-40) REVERT: D 34 MET cc_start: 0.9137 (mmt) cc_final: 0.8834 (tpp) REVERT: D 72 ASP cc_start: 0.8256 (t0) cc_final: 0.7544 (t0) REVERT: D 85 GLU cc_start: 0.9268 (pm20) cc_final: 0.9038 (pm20) REVERT: D 86 ASP cc_start: 0.9071 (m-30) cc_final: 0.8570 (m-30) REVERT: D 89 VAL cc_start: 0.9043 (t) cc_final: 0.8799 (p) REVERT: D 100 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8232 (mtp85) REVERT: D 105 GLN cc_start: 0.8222 (pm20) cc_final: 0.7776 (pp30) REVERT: E 11 LEU cc_start: 0.7596 (tt) cc_final: 0.7392 (tt) REVERT: E 45 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8661 (ttp80) REVERT: H 46 GLU cc_start: 0.8459 (tt0) cc_final: 0.7965 (pt0) REVERT: L 24 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7875 (ttm-80) REVERT: J 13 GLN cc_start: 0.8727 (mm110) cc_final: 0.8459 (mm110) REVERT: J 43 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8599 (mppt) REVERT: J 72 ASP cc_start: 0.8449 (t0) cc_final: 0.8002 (t70) outliers start: 72 outliers final: 28 residues processed: 289 average time/residue: 0.6630 time to fit residues: 215.1703 Evaluate side-chains 248 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 144 optimal weight: 0.0970 chunk 197 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 411 ASN G 80 ASN B 651 ASN I 67 ASN F 656 ASN H 13 GLN H 81 GLN J 39 GLN K 38 GLN K 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.073317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053128 restraints weight = 48079.585| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.48 r_work: 0.2557 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21141 Z= 0.122 Angle : 0.557 9.909 28906 Z= 0.265 Chirality : 0.042 0.364 3529 Planarity : 0.003 0.036 3466 Dihedral : 4.291 44.908 2631 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.86 % Allowed : 22.37 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.88 (0.18), residues: 2384 helix: 3.06 (0.28), residues: 358 sheet: 0.21 (0.19), residues: 750 loop : 0.20 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.015 0.001 TYR J 100E PHE 0.011 0.001 PHE G 383 TRP 0.010 0.001 TRP G 96 HIS 0.002 0.000 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (20977) covalent geometry : angle 0.53508 / 0.26 (28459) SS BOND : bond 0.00192 / 0.12 ( 45) SS BOND : angle 0.56332 / 0.41 ( 90) hydrogen bonds : bond 0.03595 / 2.39 ( 744) hydrogen bonds : angle 5.01290 / 3.51 ( 2046) link_ALPHA1-2 : bond 0.01067 / 0.39 ( 3) link_ALPHA1-2 : angle 2.10557 / 1.14 ( 9) link_ALPHA1-3 : bond 0.00615 / 0.35 ( 6) link_ALPHA1-3 : angle 1.30368 / 0.77 ( 18) link_ALPHA1-6 : bond 0.00424 / 0.22 ( 5) link_ALPHA1-6 : angle 1.43678 / 0.79 ( 15) link_BETA1-4 : bond 0.00357 / 0.22 ( 50) link_BETA1-4 : angle 1.23959 / 0.82 ( 150) link_NAG-ASN : bond 0.00270 / 0.16 ( 55) link_NAG-ASN : angle 1.64157 / 1.10 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: C 475 MET cc_start: 0.8550 (tpp) cc_final: 0.8258 (mpp) REVERT: A 543 ASN cc_start: 0.9476 (m-40) cc_final: 0.9155 (m110) REVERT: A 601 LYS cc_start: 0.9165 (mttm) cc_final: 0.8852 (mtmm) REVERT: G 475 MET cc_start: 0.8729 (mmm) cc_final: 0.8004 (mpp) REVERT: B 584 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8558 (mt-10) REVERT: B 632 ASP cc_start: 0.9121 (t0) cc_final: 0.8829 (t0) REVERT: B 655 LYS cc_start: 0.8731 (tptm) cc_final: 0.8373 (tptm) REVERT: B 659 ASP cc_start: 0.8647 (m-30) cc_final: 0.8410 (m-30) REVERT: F 599 SER cc_start: 0.9473 (t) cc_final: 0.9254 (p) REVERT: F 655 LYS cc_start: 0.7976 (tptt) cc_final: 0.7647 (ttpt) REVERT: D 13 GLN cc_start: 0.8873 (mp10) cc_final: 0.8379 (mm-40) REVERT: D 34 MET cc_start: 0.9122 (mmp) cc_final: 0.8833 (tpp) REVERT: D 72 ASP cc_start: 0.8217 (t0) cc_final: 0.7446 (t0) REVERT: D 86 ASP cc_start: 0.9033 (m-30) cc_final: 0.8504 (m-30) REVERT: D 89 VAL cc_start: 0.9063 (t) cc_final: 0.8825 (p) REVERT: D 100 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8299 (mtp85) REVERT: D 105 GLN cc_start: 0.8099 (pm20) cc_final: 0.7886 (pm20) REVERT: E 45 ARG cc_start: 0.8869 (ttp80) cc_final: 0.8665 (ttp80) REVERT: H 46 GLU cc_start: 0.8480 (tt0) cc_final: 0.7986 (pt0) REVERT: J 13 GLN cc_start: 0.8740 (mm110) cc_final: 0.8470 (mm110) REVERT: J 43 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8561 (mppt) REVERT: J 72 ASP cc_start: 0.8473 (t0) cc_final: 0.8016 (t70) REVERT: J 105 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8764 (mm-40) REVERT: K 79 GLN cc_start: 0.8588 (mt0) cc_final: 0.8345 (mt0) outliers start: 60 outliers final: 31 residues processed: 282 average time/residue: 0.6618 time to fit residues: 209.0991 Evaluate side-chains 250 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 189 optimal weight: 10.0000 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 411 ASN G 80 ASN F 625 ASN F 656 ASN H 13 GLN H 81 GLN L 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052709 restraints weight = 47838.335| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.52 r_work: 0.2555 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21141 Z= 0.131 Angle : 0.552 9.688 28906 Z= 0.263 Chirality : 0.042 0.357 3529 Planarity : 0.003 0.032 3466 Dihedral : 4.131 45.342 2626 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.28 % Allowed : 22.18 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.88 (0.18), residues: 2384 helix: 2.93 (0.29), residues: 365 sheet: 0.23 (0.19), residues: 753 loop : 0.21 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 18 TYR 0.015 0.001 TYR J 100E PHE 0.011 0.001 PHE G 383 TRP 0.011 0.001 TRP D 103 HIS 0.002 0.000 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20977) covalent geometry : angle 0.53062 / 0.26 (28459) SS BOND : bond 0.00243 / 0.15 ( 45) SS BOND : angle 0.54322 / 0.39 ( 90) hydrogen bonds : bond 0.03538 / 2.35 ( 744) hydrogen bonds : angle 4.87368 / 3.41 ( 2046) link_ALPHA1-2 : bond 0.01005 / 0.37 ( 3) link_ALPHA1-2 : angle 2.07994 / 1.12 ( 9) link_ALPHA1-3 : bond 0.00586 / 0.32 ( 6) link_ALPHA1-3 : angle 1.30976 / 0.77 ( 18) link_ALPHA1-6 : bond 0.00408 / 0.22 ( 5) link_ALPHA1-6 : angle 1.42753 / 0.79 ( 15) link_BETA1-4 : bond 0.00346 / 0.21 ( 50) link_BETA1-4 : angle 1.23656 / 0.82 ( 150) link_NAG-ASN : bond 0.00277 / 0.16 ( 55) link_NAG-ASN : angle 1.64189 / 1.10 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: C 475 MET cc_start: 0.8518 (tpp) cc_final: 0.8224 (mpp) REVERT: A 601 LYS cc_start: 0.9177 (mttm) cc_final: 0.8872 (mtmm) REVERT: A 617 ARG cc_start: 0.9208 (mtp85) cc_final: 0.8951 (mtp85) REVERT: G 475 MET cc_start: 0.8699 (mmm) cc_final: 0.7991 (mpp) REVERT: B 632 ASP cc_start: 0.9080 (t0) cc_final: 0.8742 (t0) REVERT: B 655 LYS cc_start: 0.8707 (tptm) cc_final: 0.8366 (tptm) REVERT: B 659 ASP cc_start: 0.8665 (m-30) cc_final: 0.8430 (m-30) REVERT: I 114 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: I 231 LYS cc_start: 0.9443 (mttt) cc_final: 0.9194 (mttm) REVERT: F 599 SER cc_start: 0.9476 (t) cc_final: 0.9261 (p) REVERT: F 621 GLU cc_start: 0.9021 (pt0) cc_final: 0.8677 (pt0) REVERT: F 655 LYS cc_start: 0.7982 (tptt) cc_final: 0.7684 (ttpt) REVERT: D 3 GLN cc_start: 0.8655 (tp40) cc_final: 0.8438 (mm-40) REVERT: D 13 GLN cc_start: 0.8876 (mp10) cc_final: 0.8408 (mm-40) REVERT: D 34 MET cc_start: 0.9129 (mmp) cc_final: 0.8848 (tpp) REVERT: D 72 ASP cc_start: 0.8196 (t0) cc_final: 0.7449 (t0) REVERT: D 86 ASP cc_start: 0.9014 (m-30) cc_final: 0.8346 (m-30) REVERT: D 89 VAL cc_start: 0.9070 (t) cc_final: 0.8818 (p) REVERT: D 100 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8315 (mtp85) REVERT: D 105 GLN cc_start: 0.8282 (pm20) cc_final: 0.8000 (pm20) REVERT: E 45 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8565 (ttp80) REVERT: E 54 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8227 (ttm-80) REVERT: E 79 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: H 46 GLU cc_start: 0.8433 (tt0) cc_final: 0.7980 (pt0) REVERT: L 24 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7745 (ttm-80) REVERT: J 13 GLN cc_start: 0.8751 (mm110) cc_final: 0.8485 (mm110) REVERT: J 43 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8530 (mppt) REVERT: J 72 ASP cc_start: 0.8489 (t0) cc_final: 0.8009 (t70) REVERT: J 105 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8805 (mm-40) outliers start: 69 outliers final: 36 residues processed: 280 average time/residue: 0.6426 time to fit residues: 202.1024 Evaluate side-chains 256 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 97 optimal weight: 0.0070 chunk 187 optimal weight: 6.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN G 80 ASN F 656 ASN H 13 GLN H 81 GLN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.073962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.053408 restraints weight = 47657.130| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.52 r_work: 0.2572 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21141 Z= 0.109 Angle : 0.546 9.632 28906 Z= 0.259 Chirality : 0.042 0.353 3529 Planarity : 0.003 0.028 3466 Dihedral : 3.995 45.620 2623 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.62 % Allowed : 23.37 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.97 (0.18), residues: 2384 helix: 3.21 (0.28), residues: 356 sheet: 0.31 (0.19), residues: 753 loop : 0.20 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 18 TYR 0.013 0.001 TYR J 100E PHE 0.011 0.001 PHE G 383 TRP 0.009 0.001 TRP I 112 HIS 0.002 0.000 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20977) covalent geometry : angle 0.52559 / 0.25 (28459) SS BOND : bond 0.00181 / 0.12 ( 45) SS BOND : angle 0.54327 / 0.40 ( 90) hydrogen bonds : bond 0.03343 / 2.22 ( 744) hydrogen bonds : angle 4.73303 / 3.31 ( 2046) link_ALPHA1-2 : bond 0.00976 / 0.37 ( 3) link_ALPHA1-2 : angle 2.05106 / 1.11 ( 9) link_ALPHA1-3 : bond 0.00611 / 0.34 ( 6) link_ALPHA1-3 : angle 1.29328 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00409 / 0.22 ( 5) link_ALPHA1-6 : angle 1.41215 / 0.78 ( 15) link_BETA1-4 : bond 0.00365 / 0.22 ( 50) link_BETA1-4 : angle 1.21451 / 0.80 ( 150) link_NAG-ASN : bond 0.00233 / 0.13 ( 55) link_NAG-ASN : angle 1.58681 / 1.06 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: C 475 MET cc_start: 0.8531 (tpp) cc_final: 0.8198 (mpp) REVERT: A 601 LYS cc_start: 0.9174 (mttm) cc_final: 0.8871 (mtmm) REVERT: G 475 MET cc_start: 0.8666 (mmm) cc_final: 0.7979 (mpp) REVERT: B 584 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8529 (mt-10) REVERT: B 632 ASP cc_start: 0.9057 (t0) cc_final: 0.8761 (t0) REVERT: B 655 LYS cc_start: 0.8671 (tptm) cc_final: 0.8335 (tptm) REVERT: B 659 ASP cc_start: 0.8681 (m-30) cc_final: 0.8448 (m-30) REVERT: I 231 LYS cc_start: 0.9444 (mttt) cc_final: 0.9204 (mttm) REVERT: F 599 SER cc_start: 0.9452 (t) cc_final: 0.9227 (p) REVERT: F 621 GLU cc_start: 0.9006 (pt0) cc_final: 0.8675 (pt0) REVERT: F 655 LYS cc_start: 0.7981 (tptt) cc_final: 0.7705 (ttpt) REVERT: D 3 GLN cc_start: 0.8653 (tp40) cc_final: 0.8423 (mm-40) REVERT: D 13 GLN cc_start: 0.8873 (mp10) cc_final: 0.8395 (mm-40) REVERT: D 34 MET cc_start: 0.9119 (mmp) cc_final: 0.8830 (tpp) REVERT: D 72 ASP cc_start: 0.8186 (t0) cc_final: 0.7390 (t0) REVERT: D 86 ASP cc_start: 0.9037 (m-30) cc_final: 0.8397 (m-30) REVERT: D 89 VAL cc_start: 0.9074 (t) cc_final: 0.8823 (p) REVERT: D 100 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8328 (mtp85) REVERT: D 105 GLN cc_start: 0.8315 (pm20) cc_final: 0.8055 (pm20) REVERT: E 54 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8229 (ttm-80) REVERT: H 46 GLU cc_start: 0.8438 (tt0) cc_final: 0.8031 (pt0) REVERT: L 24 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7756 (ttm-80) REVERT: L 70 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8214 (mm-30) REVERT: J 13 GLN cc_start: 0.8766 (mm110) cc_final: 0.8504 (mm110) REVERT: J 43 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8551 (mppt) REVERT: J 72 ASP cc_start: 0.8497 (t0) cc_final: 0.8059 (t70) REVERT: J 105 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8807 (mm-40) REVERT: K 24 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7706 (mtm-85) REVERT: K 79 GLN cc_start: 0.8630 (mt0) cc_final: 0.8257 (mt0) REVERT: K 103 LYS cc_start: 0.8774 (tppp) cc_final: 0.8345 (tppp) outliers start: 55 outliers final: 35 residues processed: 275 average time/residue: 0.6660 time to fit residues: 205.0112 Evaluate side-chains 257 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 61 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 32 optimal weight: 0.0000 chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 80 ASN F 656 ASN D 13 GLN H 13 GLN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.052681 restraints weight = 47764.438| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.52 r_work: 0.2554 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21141 Z= 0.147 Angle : 0.567 9.630 28906 Z= 0.267 Chirality : 0.043 0.354 3529 Planarity : 0.003 0.048 3466 Dihedral : 4.010 45.741 2623 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.90 % Allowed : 23.32 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.95 (0.18), residues: 2384 helix: 2.99 (0.28), residues: 369 sheet: 0.30 (0.19), residues: 753 loop : 0.22 (0.19), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 18 TYR 0.014 0.001 TYR J 100E PHE 0.011 0.001 PHE G 383 TRP 0.011 0.001 TRP D 103 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (20977) covalent geometry : angle 0.54584 / 0.26 (28459) SS BOND : bond 0.00213 / 0.14 ( 45) SS BOND : angle 0.57270 / 0.42 ( 90) hydrogen bonds : bond 0.03480 / 2.31 ( 744) hydrogen bonds : angle 4.73213 / 3.31 ( 2046) link_ALPHA1-2 : bond 0.00930 / 0.34 ( 3) link_ALPHA1-2 : angle 2.04887 / 1.11 ( 9) link_ALPHA1-3 : bond 0.00545 / 0.30 ( 6) link_ALPHA1-3 : angle 1.32105 / 0.78 ( 18) link_ALPHA1-6 : bond 0.00383 / 0.20 ( 5) link_ALPHA1-6 : angle 1.41754 / 0.79 ( 15) link_BETA1-4 : bond 0.00337 / 0.21 ( 50) link_BETA1-4 : angle 1.23271 / 0.81 ( 150) link_NAG-ASN : bond 0.00292 / 0.17 ( 55) link_NAG-ASN : angle 1.63747 / 1.10 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8332 (mp10) REVERT: C 475 MET cc_start: 0.8553 (tpp) cc_final: 0.8197 (mpp) REVERT: A 601 LYS cc_start: 0.9180 (mttm) cc_final: 0.8871 (mtmm) REVERT: A 617 ARG cc_start: 0.9186 (mtp85) cc_final: 0.8846 (mtp85) REVERT: A 621 GLU cc_start: 0.9039 (tt0) cc_final: 0.7972 (tm-30) REVERT: G 475 MET cc_start: 0.8686 (mmm) cc_final: 0.7989 (mpp) REVERT: B 584 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8560 (mt-10) REVERT: B 632 ASP cc_start: 0.9038 (t0) cc_final: 0.8731 (t0) REVERT: B 655 LYS cc_start: 0.8660 (tptm) cc_final: 0.8449 (tptp) REVERT: I 114 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: I 231 LYS cc_start: 0.9444 (mttt) cc_final: 0.9204 (mttm) REVERT: F 621 GLU cc_start: 0.9000 (pt0) cc_final: 0.8611 (pt0) REVERT: F 655 LYS cc_start: 0.8032 (tptt) cc_final: 0.7737 (tppt) REVERT: D 3 GLN cc_start: 0.8668 (tp40) cc_final: 0.8431 (mm-40) REVERT: D 13 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8481 (mm-40) REVERT: D 34 MET cc_start: 0.9141 (mmp) cc_final: 0.8915 (tpp) REVERT: D 72 ASP cc_start: 0.8189 (t0) cc_final: 0.7405 (t0) REVERT: D 89 VAL cc_start: 0.9067 (t) cc_final: 0.8812 (p) REVERT: D 100 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8275 (mtp85) REVERT: D 105 GLN cc_start: 0.8344 (pm20) cc_final: 0.8091 (pm20) REVERT: E 54 ARG cc_start: 0.8688 (ttm110) cc_final: 0.8251 (ttm-80) REVERT: H 46 GLU cc_start: 0.8447 (tt0) cc_final: 0.8040 (pt0) REVERT: L 24 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7802 (ttm-80) REVERT: J 13 GLN cc_start: 0.8772 (mm110) cc_final: 0.8512 (mm110) REVERT: J 72 ASP cc_start: 0.8501 (t0) cc_final: 0.8059 (t70) REVERT: J 105 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8855 (mm-40) REVERT: K 24 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7753 (mtm-85) REVERT: K 103 LYS cc_start: 0.8768 (tppp) cc_final: 0.8286 (tppp) outliers start: 61 outliers final: 42 residues processed: 263 average time/residue: 0.6541 time to fit residues: 191.7910 Evaluate side-chains 256 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 209 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 80 ASN G 114 GLN F 656 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052610 restraints weight = 48077.011| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.53 r_work: 0.2554 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21141 Z= 0.143 Angle : 0.571 9.629 28906 Z= 0.270 Chirality : 0.043 0.354 3529 Planarity : 0.003 0.046 3466 Dihedral : 4.006 45.897 2623 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.67 % Allowed : 23.51 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.94 (0.18), residues: 2384 helix: 2.99 (0.28), residues: 369 sheet: 0.32 (0.19), residues: 753 loop : 0.20 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 18 TYR 0.014 0.001 TYR J 100E PHE 0.011 0.001 PHE G 383 TRP 0.008 0.001 TRP G 96 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (20977) covalent geometry : angle 0.55068 / 0.27 (28459) SS BOND : bond 0.00213 / 0.14 ( 45) SS BOND : angle 0.54746 / 0.38 ( 90) hydrogen bonds : bond 0.03467 / 2.30 ( 744) hydrogen bonds : angle 4.70898 / 3.29 ( 2046) link_ALPHA1-2 : bond 0.00907 / 0.33 ( 3) link_ALPHA1-2 : angle 2.04123 / 1.10 ( 9) link_ALPHA1-3 : bond 0.00544 / 0.30 ( 6) link_ALPHA1-3 : angle 1.31708 / 0.78 ( 18) link_ALPHA1-6 : bond 0.00390 / 0.21 ( 5) link_ALPHA1-6 : angle 1.41971 / 0.79 ( 15) link_BETA1-4 : bond 0.00334 / 0.20 ( 50) link_BETA1-4 : angle 1.23441 / 0.81 ( 150) link_NAG-ASN : bond 0.00283 / 0.17 ( 55) link_NAG-ASN : angle 1.63863 / 1.10 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8326 (mp10) REVERT: C 475 MET cc_start: 0.8540 (tpp) cc_final: 0.8194 (mpp) REVERT: A 601 LYS cc_start: 0.9179 (mttm) cc_final: 0.8870 (mtmm) REVERT: G 475 MET cc_start: 0.8695 (mmm) cc_final: 0.8003 (mpp) REVERT: B 584 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8535 (mt-10) REVERT: B 632 ASP cc_start: 0.9083 (t0) cc_final: 0.8748 (t0) REVERT: B 633 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8776 (mtpt) REVERT: B 655 LYS cc_start: 0.8646 (tptm) cc_final: 0.8433 (tptp) REVERT: I 114 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: I 231 LYS cc_start: 0.9441 (mttt) cc_final: 0.9201 (mttm) REVERT: F 621 GLU cc_start: 0.8989 (pt0) cc_final: 0.8602 (pt0) REVERT: F 655 LYS cc_start: 0.8023 (tptt) cc_final: 0.7732 (tppt) REVERT: D 3 GLN cc_start: 0.8673 (tp40) cc_final: 0.8428 (mm-40) REVERT: D 13 GLN cc_start: 0.9095 (mp10) cc_final: 0.8790 (tp40) REVERT: D 34 MET cc_start: 0.9137 (mmp) cc_final: 0.8910 (tpp) REVERT: D 72 ASP cc_start: 0.8191 (t0) cc_final: 0.7397 (t0) REVERT: D 86 ASP cc_start: 0.8968 (m-30) cc_final: 0.8452 (m-30) REVERT: D 89 VAL cc_start: 0.9069 (t) cc_final: 0.8807 (p) REVERT: D 100 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8281 (mtp85) REVERT: D 105 GLN cc_start: 0.8396 (pm20) cc_final: 0.8165 (pm20) REVERT: E 54 ARG cc_start: 0.8700 (ttm110) cc_final: 0.8258 (ttm-80) REVERT: H 46 GLU cc_start: 0.8449 (tt0) cc_final: 0.8041 (pt0) REVERT: L 24 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7902 (ttm-80) REVERT: L 70 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8189 (mm-30) REVERT: J 13 GLN cc_start: 0.8777 (mm110) cc_final: 0.8514 (mm110) REVERT: J 43 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8502 (mppt) REVERT: J 72 ASP cc_start: 0.8498 (t0) cc_final: 0.8059 (t70) REVERT: J 105 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8844 (mm-40) REVERT: K 24 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7689 (mtm-85) REVERT: K 103 LYS cc_start: 0.8765 (tppp) cc_final: 0.8272 (tppp) outliers start: 56 outliers final: 42 residues processed: 257 average time/residue: 0.6826 time to fit residues: 195.4959 Evaluate side-chains 260 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 156 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN G 80 ASN F 656 ASN H 3 GLN H 13 GLN H 81 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.051997 restraints weight = 47811.858| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.53 r_work: 0.2539 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21141 Z= 0.170 Angle : 0.588 9.641 28906 Z= 0.279 Chirality : 0.043 0.354 3529 Planarity : 0.003 0.062 3466 Dihedral : 4.051 46.198 2623 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.71 % Allowed : 23.47 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.88 (0.18), residues: 2384 helix: 2.94 (0.28), residues: 369 sheet: 0.29 (0.19), residues: 744 loop : 0.14 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 18 TYR 0.014 0.001 TYR J 100E PHE 0.012 0.001 PHE G 383 TRP 0.013 0.001 TRP D 103 HIS 0.002 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (20977) covalent geometry : angle 0.56743 / 0.27 (28459) SS BOND : bond 0.00244 / 0.15 ( 45) SS BOND : angle 0.60423 / 0.44 ( 90) hydrogen bonds : bond 0.03608 / 2.39 ( 744) hydrogen bonds : angle 4.73627 / 3.31 ( 2046) link_ALPHA1-2 : bond 0.00838 / 0.31 ( 3) link_ALPHA1-2 : angle 2.03225 / 1.09 ( 9) link_ALPHA1-3 : bond 0.00495 / 0.27 ( 6) link_ALPHA1-3 : angle 1.33664 / 0.79 ( 18) link_ALPHA1-6 : bond 0.00367 / 0.19 ( 5) link_ALPHA1-6 : angle 1.42034 / 0.79 ( 15) link_BETA1-4 : bond 0.00312 / 0.19 ( 50) link_BETA1-4 : angle 1.25873 / 0.83 ( 150) link_NAG-ASN : bond 0.00341 / 0.20 ( 55) link_NAG-ASN : angle 1.68907 / 1.13 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8366 (mp10) REVERT: C 475 MET cc_start: 0.8531 (tpp) cc_final: 0.8180 (mpp) REVERT: A 601 LYS cc_start: 0.9190 (mttm) cc_final: 0.8877 (mtmm) REVERT: G 475 MET cc_start: 0.8707 (mmm) cc_final: 0.8012 (mpp) REVERT: B 584 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8564 (mt-10) REVERT: B 632 ASP cc_start: 0.9019 (t70) cc_final: 0.8734 (t0) REVERT: B 633 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8790 (mtpt) REVERT: B 655 LYS cc_start: 0.8647 (tptm) cc_final: 0.8444 (tptp) REVERT: I 114 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8084 (mp10) REVERT: I 231 LYS cc_start: 0.9441 (mttt) cc_final: 0.9200 (mttm) REVERT: F 621 GLU cc_start: 0.8990 (pt0) cc_final: 0.8610 (pt0) REVERT: F 655 LYS cc_start: 0.8001 (tptt) cc_final: 0.7682 (tppt) REVERT: D 3 GLN cc_start: 0.8707 (tp40) cc_final: 0.8454 (mm-40) REVERT: D 12 VAL cc_start: 0.9616 (t) cc_final: 0.9364 (p) REVERT: D 13 GLN cc_start: 0.9069 (mp10) cc_final: 0.8592 (mm-40) REVERT: D 18 LEU cc_start: 0.8602 (tt) cc_final: 0.8039 (tp) REVERT: D 72 ASP cc_start: 0.8251 (t0) cc_final: 0.7415 (t0) REVERT: D 82 MET cc_start: 0.8767 (ptp) cc_final: 0.8182 (pmm) REVERT: D 89 VAL cc_start: 0.9076 (t) cc_final: 0.8812 (p) REVERT: D 100 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8284 (mtp85) REVERT: D 105 GLN cc_start: 0.8401 (pm20) cc_final: 0.8173 (pm20) REVERT: E 54 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8286 (ttm-80) REVERT: H 46 GLU cc_start: 0.8436 (tt0) cc_final: 0.8049 (pt0) REVERT: L 24 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7897 (ttm-80) REVERT: J 13 GLN cc_start: 0.8781 (mm110) cc_final: 0.8519 (mm110) REVERT: J 43 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8484 (mppt) REVERT: J 72 ASP cc_start: 0.8513 (t0) cc_final: 0.8074 (t70) REVERT: J 105 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8919 (mm-40) REVERT: K 24 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7688 (mtm-85) REVERT: K 103 LYS cc_start: 0.8741 (tppp) cc_final: 0.8240 (tppp) outliers start: 57 outliers final: 41 residues processed: 256 average time/residue: 0.6901 time to fit residues: 196.9571 Evaluate side-chains 257 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 199 optimal weight: 0.1980 chunk 99 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 80 ASN F 625 ASN F 656 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.052981 restraints weight = 47826.803| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.53 r_work: 0.2565 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21141 Z= 0.120 Angle : 0.569 9.666 28906 Z= 0.269 Chirality : 0.042 0.353 3529 Planarity : 0.003 0.044 3466 Dihedral : 4.002 46.444 2623 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.05 % Allowed : 24.23 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.93 (0.18), residues: 2384 helix: 2.99 (0.28), residues: 369 sheet: 0.30 (0.19), residues: 753 loop : 0.18 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 18 TYR 0.012 0.001 TYR J 100E PHE 0.011 0.001 PHE G 383 TRP 0.009 0.001 TRP G 96 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (20977) covalent geometry : angle 0.54969 / 0.27 (28459) SS BOND : bond 0.00243 / 0.15 ( 45) SS BOND : angle 0.53026 / 0.37 ( 90) hydrogen bonds : bond 0.03340 / 2.22 ( 744) hydrogen bonds : angle 4.63776 / 3.24 ( 2046) link_ALPHA1-2 : bond 0.00877 / 0.32 ( 3) link_ALPHA1-2 : angle 1.98907 / 1.07 ( 9) link_ALPHA1-3 : bond 0.00566 / 0.31 ( 6) link_ALPHA1-3 : angle 1.28888 / 0.77 ( 18) link_ALPHA1-6 : bond 0.00393 / 0.21 ( 5) link_ALPHA1-6 : angle 1.41278 / 0.79 ( 15) link_BETA1-4 : bond 0.00337 / 0.20 ( 50) link_BETA1-4 : angle 1.21847 / 0.80 ( 150) link_NAG-ASN : bond 0.00238 / 0.13 ( 55) link_NAG-ASN : angle 1.60086 / 1.07 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8335 (mp10) REVERT: C 475 MET cc_start: 0.8514 (tpp) cc_final: 0.8171 (mpp) REVERT: A 601 LYS cc_start: 0.9169 (mttm) cc_final: 0.8863 (mtmm) REVERT: G 475 MET cc_start: 0.8631 (mmm) cc_final: 0.7961 (mpp) REVERT: B 632 ASP cc_start: 0.9009 (t70) cc_final: 0.8722 (t0) REVERT: B 633 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8749 (mtpt) REVERT: I 114 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: I 231 LYS cc_start: 0.9441 (mttt) cc_final: 0.9196 (mttm) REVERT: F 621 GLU cc_start: 0.8983 (pt0) cc_final: 0.8616 (pt0) REVERT: F 655 LYS cc_start: 0.7951 (tptt) cc_final: 0.7646 (ttpt) REVERT: D 3 GLN cc_start: 0.8699 (tp40) cc_final: 0.8483 (mm-40) REVERT: D 12 VAL cc_start: 0.9615 (t) cc_final: 0.9370 (p) REVERT: D 13 GLN cc_start: 0.9043 (mp10) cc_final: 0.8577 (mm-40) REVERT: D 18 LEU cc_start: 0.8529 (tt) cc_final: 0.8040 (tp) REVERT: D 72 ASP cc_start: 0.8232 (t0) cc_final: 0.7415 (t0) REVERT: D 82 MET cc_start: 0.8684 (ptp) cc_final: 0.8268 (pmm) REVERT: D 89 VAL cc_start: 0.9086 (t) cc_final: 0.8819 (p) REVERT: D 100 ARG cc_start: 0.8654 (mtm-85) cc_final: 0.8251 (mtp85) REVERT: D 105 GLN cc_start: 0.8403 (pm20) cc_final: 0.8172 (pm20) REVERT: E 54 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8251 (ttm-80) REVERT: E 103 LYS cc_start: 0.8766 (tppp) cc_final: 0.8565 (tptp) REVERT: H 46 GLU cc_start: 0.8407 (tt0) cc_final: 0.8000 (pt0) REVERT: L 24 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7867 (ttm-80) REVERT: L 70 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8223 (mm-30) REVERT: J 13 GLN cc_start: 0.8787 (mm110) cc_final: 0.8525 (mm110) REVERT: J 43 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8488 (mppt) REVERT: J 72 ASP cc_start: 0.8508 (t0) cc_final: 0.8069 (t70) REVERT: J 105 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8915 (mm-40) REVERT: K 24 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7688 (mtm-85) REVERT: K 103 LYS cc_start: 0.8742 (tppp) cc_final: 0.8252 (tppp) outliers start: 43 outliers final: 36 residues processed: 250 average time/residue: 0.6897 time to fit residues: 192.6161 Evaluate side-chains 253 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 95 optimal weight: 0.0470 chunk 196 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 209 optimal weight: 0.0270 chunk 80 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 80 ASN F 656 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.054033 restraints weight = 47736.388| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.53 r_work: 0.2591 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21141 Z= 0.099 Angle : 0.559 10.220 28906 Z= 0.264 Chirality : 0.042 0.353 3529 Planarity : 0.003 0.048 3466 Dihedral : 3.876 46.219 2621 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.67 % Allowed : 24.80 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.96 (0.18), residues: 2384 helix: 3.08 (0.28), residues: 367 sheet: 0.29 (0.19), residues: 762 loop : 0.22 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 18 TYR 0.011 0.001 TYR J 100E PHE 0.010 0.001 PHE G 383 TRP 0.013 0.001 TRP D 103 HIS 0.002 0.000 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (20977) covalent geometry : angle 0.54133 / 0.26 (28459) SS BOND : bond 0.00163 / 0.10 ( 45) SS BOND : angle 0.51915 / 0.38 ( 90) hydrogen bonds : bond 0.03127 / 2.09 ( 744) hydrogen bonds : angle 4.51317 / 3.15 ( 2046) link_ALPHA1-2 : bond 0.00880 / 0.33 ( 3) link_ALPHA1-2 : angle 1.92572 / 1.04 ( 9) link_ALPHA1-3 : bond 0.00605 / 0.33 ( 6) link_ALPHA1-3 : angle 1.28049 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00411 / 0.22 ( 5) link_ALPHA1-6 : angle 1.41883 / 0.79 ( 15) link_BETA1-4 : bond 0.00376 / 0.23 ( 50) link_BETA1-4 : angle 1.19185 / 0.79 ( 150) link_NAG-ASN : bond 0.00206 / 0.11 ( 55) link_NAG-ASN : angle 1.50933 / 1.01 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5581.98 seconds wall clock time: 96 minutes 21.99 seconds (5781.99 seconds total)