Starting phenix.real_space_refine on Mon Sep 14 03:52:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22ov_68575/09_2026/22ov_68575_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/22ov_68575/09_2026/22ov_68575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22ov_68575/09_2026/22ov_68575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22ov_68575/09_2026/22ov_68575.map" model { file = "/net/cci-nas-00/data/ceres_data/22ov_68575/09_2026/22ov_68575_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22ov_68575/09_2026/22ov_68575_neut.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 108 5.16 5 C 17139 2.51 5 N 4278 2.21 5 O 5439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26964 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 8391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8391 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 58, 'TRANS': 1010} Chain breaks: 3 Chain: "B" Number of atoms: 8391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8391 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 58, 'TRANS': 1010} Chain breaks: 3 Chain: "C" Number of atoms: 8391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8391 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 58, 'TRANS': 1010} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.01, per 1000 atoms: 0.22 Number of scatterers: 26964 At special positions: 0 Unit cell: (156.56, 150.48, 177.08, 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 108 16.00 O 5439 8.00 N 4278 7.00 C 17139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 G 4 " - " MAN G 5 " " MAN T 4 " - " MAN T 5 " " MAN g 4 " - " MAN g 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA T 3 " - " MAN T 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " NAG-ASN " NAG A1301 " - " ASN A 99 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 185 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 331 " " NAG B1301 " - " ASN B 99 " " NAG B1302 " - " ASN B 149 " " NAG B1303 " - " ASN B 185 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 331 " " NAG C1301 " - " ASN C 99 " " NAG C1302 " - " ASN C 149 " " NAG C1303 " - " ASN C 185 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 331 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 354 " " NAG J 1 " - " ASN A 529 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 61 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 165 " " NAG T 1 " - " ASN B 234 " " NAG U 1 " - " ASN B 282 " " NAG V 1 " - " ASN B 354 " " NAG W 1 " - " ASN B 529 " " NAG X 1 " - " ASN B 709 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B1074 " " NAG b 1 " - " ASN B1098 " " NAG c 1 " - " ASN B1134 " " NAG d 1 " - " ASN C 61 " " NAG e 1 " - " ASN C 122 " " NAG f 1 " - " ASN C 165 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 282 " " NAG i 1 " - " ASN C 354 " " NAG j 1 " - " ASN C 529 " " NAG k 1 " - " ASN C 709 " " NAG l 1 " - " ASN C 717 " " NAG m 1 " - " ASN C 801 " " NAG n 1 " - " ASN C1074 " " NAG o 1 " - " ASN C1098 " " NAG p 1 " - " ASN C1134 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 978.0 milliseconds 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 27.2% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.529A pdb=" N VAL A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.203A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.657A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.850A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 417 through 422 removed outlier: 4.000A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.970A pdb=" N GLN A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.892A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.520A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 831 removed outlier: 3.948A pdb=" N ALA A 829 " --> pdb=" O LYS A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.532A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.438A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.907A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.676A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.518A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.407A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.529A pdb=" N VAL B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.203A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.657A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.850A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 417 through 422 removed outlier: 4.000A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.970A pdb=" N GLN B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 636 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.892A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.520A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 831 removed outlier: 3.948A pdb=" N ALA B 829 " --> pdb=" O LYS B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.532A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.438A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.906A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.677A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.519A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.406A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.529A pdb=" N VAL C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.203A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.657A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.850A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.000A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.970A pdb=" N GLN C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 636 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.892A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.520A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 831 removed outlier: 3.947A pdb=" N ALA C 829 " --> pdb=" O LYS C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.532A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.438A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.907A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.677A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.518A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.406A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.190A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.785A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.574A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.736A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.543A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.231A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.955A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.034A pdb=" N LYS A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR A 696 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.664A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.058A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.861A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.191A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.784A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.574A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.735A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.543A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.230A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.956A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.034A pdb=" N LYS B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 696 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.663A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.861A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.190A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.784A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.574A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.736A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.543A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.231A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.954A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.034A pdb=" N LYS C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR C 696 " --> pdb=" O LYS C 654 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.664A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.861A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 2919 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: 6.16 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8270 1.35 - 1.47: 7211 1.47 - 1.59: 11966 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 27585 Sorted by residual: bond pdb=" C PHE B 220 " pdb=" N SER B 221 " ideal model delta sigma weight residual 1.331 1.383 -0.051 1.28e-02 6.10e+03 1.62e+01 bond pdb=" C PHE C 220 " pdb=" N SER C 221 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.28e-02 6.10e+03 1.61e+01 bond pdb=" C PHE A 220 " pdb=" N SER A 221 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.28e-02 6.10e+03 1.57e+01 bond pdb=" N ASN C 657 " pdb=" CA ASN C 657 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.70e+00 bond pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.66e+00 ... (remaining 27580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 36013 2.04 - 4.07: 1365 4.07 - 6.11: 170 6.11 - 8.14: 21 8.14 - 10.18: 3 Bond angle restraints: 37572 Sorted by residual: angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 116.54 110.21 6.33 1.15e+00 7.56e-01 3.03e+01 angle pdb=" C PHE A 32 " pdb=" CA PHE A 32 " pdb=" CB PHE A 32 " ideal model delta sigma weight residual 116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" O THR C 167 " pdb=" C THR C 167 " pdb=" N PHE C 168 " ideal model delta sigma weight residual 122.23 115.53 6.70 1.30e+00 5.92e-01 2.66e+01 angle pdb=" O THR B 167 " pdb=" C THR B 167 " pdb=" N PHE B 168 " ideal model delta sigma weight residual 122.23 115.55 6.68 1.30e+00 5.92e-01 2.64e+01 ... (remaining 37567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 16855 21.26 - 42.53: 851 42.53 - 63.79: 105 63.79 - 85.05: 198 85.05 - 106.32: 111 Dihedral angle restraints: 18120 sinusoidal: 8769 harmonic: 9351 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -123.63 37.63 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -123.61 37.61 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -123.59 37.59 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 18117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4111 0.090 - 0.179: 470 0.179 - 0.269: 49 0.269 - 0.359: 5 0.359 - 0.449: 6 Chirality restraints: 4641 Sorted by residual: chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 5.03e+02 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 5.00e+02 chirality pdb=" C1 MAN g 4 " pdb=" O3 BMA g 3 " pdb=" C2 MAN g 4 " pdb=" O5 MAN g 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 4.97e+02 ... (remaining 4638 not shown) Planarity restraints: 4713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " 0.248 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG B1301 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.170 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " -0.348 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.248 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG A1301 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.348 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.248 2.00e-02 2.50e+03 2.08e-01 5.41e+02 pdb=" C7 NAG C1301 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.002 2.00e-02 2.50e+03 ... (remaining 4710 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2156 2.75 - 3.29: 25932 3.29 - 3.82: 42610 3.82 - 4.36: 49160 4.36 - 4.90: 86057 Nonbonded interactions: 205915 Sorted by model distance: nonbonded pdb=" NH1 ARG A 357 " pdb=" O PRO B 230 " model vdw 2.209 3.120 nonbonded pdb=" O PRO A 230 " pdb=" NH1 ARG C 357 " model vdw 2.211 3.120 nonbonded pdb=" OH TYR A 904 " pdb=" CG1 VAL C1094 " model vdw 2.258 3.460 nonbonded pdb=" CG1 VAL B1094 " pdb=" OH TYR C 904 " model vdw 2.259 3.460 nonbonded pdb=" CG1 VAL A1094 " pdb=" OH TYR B 904 " model vdw 2.262 3.460 ... (remaining 205910 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'j' selection = chain 'n' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'G' selection = chain 'T' selection = chain 'g' } 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: 9.480 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.900 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27759 Z= 0.308 Angle : 0.997 12.890 38055 Z= 0.495 Chirality : 0.057 0.449 4641 Planarity : 0.012 0.208 4650 Dihedral : 17.385 106.317 11997 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.14), residues: 3183 helix: 2.20 (0.20), residues: 684 sheet: 0.09 (0.20), residues: 597 loop : -1.85 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 102 TYR 0.022 0.002 TYR A 265 PHE 0.039 0.002 PHE B 906 TRP 0.047 0.003 TRP A 436 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.28 (27585) covalent geometry : angle 0.86010 / 0.47 (37572) SS BOND : bond 0.00266 / 0.18 ( 39) SS BOND : angle 1.48218 / 0.98 ( 78) hydrogen bonds : bond 0.16186 / 10.56 ( 1015) hydrogen bonds : angle 7.02385 / 4.93 ( 2919) link_ALPHA1-2 : bond 0.04486 / 2.25 ( 3) link_ALPHA1-2 : angle 7.19043 / 3.27 ( 9) link_ALPHA1-3 : bond 0.04749 / 2.38 ( 3) link_ALPHA1-3 : angle 3.57303 / 1.60 ( 9) link_BETA1-4 : bond 0.04637 / 2.99 ( 66) link_BETA1-4 : angle 6.14837 / 4.13 ( 198) link_NAG-ASN : bond 0.00653 / 0.40 ( 63) link_NAG-ASN : angle 3.05260 / 2.02 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 561 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0322 (tmm) cc_final: -0.1488 (tmm) REVERT: A 190 ARG cc_start: 0.6805 (ttm110) cc_final: 0.6573 (mtp85) REVERT: A 221 SER cc_start: 0.8135 (t) cc_final: 0.7866 (m) REVERT: A 359 SER cc_start: 0.7150 (p) cc_final: 0.6672 (t) REVERT: A 365 TYR cc_start: 0.7045 (m-80) cc_final: 0.6710 (m-80) REVERT: A 556 ASN cc_start: 0.7343 (p0) cc_final: 0.7142 (p0) REVERT: A 613 GLN cc_start: 0.8044 (mt0) cc_final: 0.7821 (mt0) REVERT: A 660 TYR cc_start: 0.8261 (m-80) cc_final: 0.7740 (m-80) REVERT: A 755 GLN cc_start: 0.7275 (tt0) cc_final: 0.7070 (tt0) REVERT: A 819 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 1084 ASP cc_start: 0.7728 (t70) cc_final: 0.7224 (t0) REVERT: A 1092 GLU cc_start: 0.7506 (tp30) cc_final: 0.7121 (tp30) REVERT: B 51 THR cc_start: 0.7559 (t) cc_final: 0.7335 (p) REVERT: B 153 MET cc_start: 0.1366 (tmm) cc_final: 0.0620 (tmm) REVERT: B 177 MET cc_start: 0.4714 (mmm) cc_final: 0.4372 (mmm) REVERT: B 309 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 364 ASP cc_start: 0.7430 (t70) cc_final: 0.7198 (t0) REVERT: B 424 LYS cc_start: 0.7014 (tppt) cc_final: 0.6609 (tppt) REVERT: B 534 VAL cc_start: 0.7765 (m) cc_final: 0.7544 (p) REVERT: B 646 ARG cc_start: 0.8306 (mtm180) cc_final: 0.8055 (mtm180) REVERT: B 660 TYR cc_start: 0.8185 (m-80) cc_final: 0.7660 (m-80) REVERT: B 931 ILE cc_start: 0.7772 (mm) cc_final: 0.7501 (tp) REVERT: B 1010 GLN cc_start: 0.7967 (mt0) cc_final: 0.7749 (mm-40) REVERT: B 1073 LYS cc_start: 0.7953 (tttt) cc_final: 0.7634 (mtpp) REVERT: B 1084 ASP cc_start: 0.7925 (t70) cc_final: 0.7497 (t0) REVERT: B 1092 GLU cc_start: 0.7436 (tp30) cc_final: 0.7206 (tp30) REVERT: C 51 THR cc_start: 0.7472 (t) cc_final: 0.7235 (p) REVERT: C 153 MET cc_start: 0.1609 (tmm) cc_final: 0.1086 (tmm) REVERT: C 309 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7586 (mm-30) REVERT: C 340 GLU cc_start: 0.6451 (mp0) cc_final: 0.5851 (mp0) REVERT: C 359 SER cc_start: 0.6815 (p) cc_final: 0.6276 (t) REVERT: C 512 VAL cc_start: 0.6882 (t) cc_final: 0.6367 (m) REVERT: C 578 ASP cc_start: 0.6627 (t70) cc_final: 0.6125 (t70) REVERT: C 646 ARG cc_start: 0.8353 (mtm180) cc_final: 0.8143 (mtm180) REVERT: C 660 TYR cc_start: 0.8248 (m-80) cc_final: 0.7820 (m-80) REVERT: C 819 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7091 (mt-10) REVERT: C 1072 GLU cc_start: 0.8360 (pm20) cc_final: 0.8011 (pm20) REVERT: C 1073 LYS cc_start: 0.7896 (tttt) cc_final: 0.7635 (ttmm) REVERT: C 1092 GLU cc_start: 0.7559 (tp30) cc_final: 0.7203 (tp30) outliers start: 3 outliers final: 2 residues processed: 564 average time/residue: 0.5984 time to fit residues: 393.7814 Evaluate side-chains 482 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 185 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 422 ASN A 437 ASN A 564 GLN A 644 GLN A 755 GLN A 856 ASN A 935 GLN A1005 GLN A1048 HIS B 87 ASN B 437 ASN B 949 GLN C 422 ASN C 437 ASN C 644 GLN C 804 GLN C 949 GLN C1048 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.181899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.143116 restraints weight = 37294.924| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.21 r_work: 0.3762 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27759 Z= 0.170 Angle : 0.774 9.579 38055 Z= 0.366 Chirality : 0.050 0.248 4641 Planarity : 0.005 0.057 4650 Dihedral : 12.099 72.164 6229 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.78 % Allowed : 8.03 % Favored : 90.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.56 (0.14), residues: 3183 helix: 2.05 (0.20), residues: 696 sheet: 0.03 (0.19), residues: 714 loop : -1.63 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 355 TYR 0.023 0.002 TYR B 505 PHE 0.032 0.002 PHE A 172 TRP 0.015 0.002 TRP A 353 HIS 0.007 0.002 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (27585) covalent geometry : angle 0.73093 / 0.36 (37572) SS BOND : bond 0.00271 / 0.16 ( 39) SS BOND : angle 1.80022 / 1.22 ( 78) hydrogen bonds : bond 0.06796 / 4.44 ( 1015) hydrogen bonds : angle 5.82038 / 4.04 ( 2919) link_ALPHA1-2 : bond 0.00840 / 0.42 ( 3) link_ALPHA1-2 : angle 1.56308 / 0.70 ( 9) link_ALPHA1-3 : bond 0.01631 / 0.82 ( 3) link_ALPHA1-3 : angle 1.97071 / 0.90 ( 9) link_BETA1-4 : bond 0.00825 / 0.59 ( 66) link_BETA1-4 : angle 2.72483 / 1.87 ( 198) link_NAG-ASN : bond 0.00787 / 0.52 ( 63) link_NAG-ASN : angle 2.23212 / 1.48 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 507 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0416 (tmm) cc_final: -0.1355 (tmm) REVERT: A 190 ARG cc_start: 0.7413 (ttm110) cc_final: 0.7069 (ttm110) REVERT: A 309 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 512 VAL cc_start: 0.8774 (t) cc_final: 0.8489 (m) REVERT: A 1084 ASP cc_start: 0.7765 (t70) cc_final: 0.7500 (t0) REVERT: B 33 THR cc_start: 0.8084 (p) cc_final: 0.7876 (p) REVERT: B 96 GLU cc_start: 0.6047 (pt0) cc_final: 0.5607 (mt-10) REVERT: B 153 MET cc_start: 0.0707 (tmm) cc_final: -0.0097 (tmm) REVERT: B 177 MET cc_start: 0.4443 (mmm) cc_final: 0.4016 (mmm) REVERT: B 359 SER cc_start: 0.8149 (p) cc_final: 0.7938 (t) REVERT: B 424 LYS cc_start: 0.8262 (tppt) cc_final: 0.8025 (tppt) REVERT: B 635 VAL cc_start: 0.8338 (t) cc_final: 0.8133 (p) REVERT: B 931 ILE cc_start: 0.8567 (mm) cc_final: 0.8358 (tp) REVERT: B 1084 ASP cc_start: 0.7802 (t70) cc_final: 0.7558 (t0) REVERT: C 153 MET cc_start: 0.1002 (tmm) cc_final: 0.0558 (tmm) REVERT: C 359 SER cc_start: 0.7914 (p) cc_final: 0.7679 (t) REVERT: C 424 LYS cc_start: 0.8149 (tppt) cc_final: 0.7813 (tppt) REVERT: C 512 VAL cc_start: 0.8756 (t) cc_final: 0.8517 (m) REVERT: C 819 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 931 ILE cc_start: 0.8774 (mm) cc_final: 0.8510 (tp) outliers start: 50 outliers final: 20 residues processed: 530 average time/residue: 0.5739 time to fit residues: 357.1983 Evaluate side-chains 493 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 473 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 47 optimal weight: 0.0770 chunk 146 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 259 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 437 ASN A 755 GLN B 218 GLN B 437 ASN B 804 GLN B 935 GLN B 949 GLN C 87 ASN C 394 ASN C 755 GLN C 949 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.180912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.141382 restraints weight = 36969.659| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.37 r_work: 0.3732 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27759 Z= 0.151 Angle : 0.692 9.335 38055 Z= 0.335 Chirality : 0.048 0.246 4641 Planarity : 0.005 0.048 4650 Dihedral : 7.809 58.381 6227 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.03 % Allowed : 10.34 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.14), residues: 3183 helix: 2.16 (0.20), residues: 690 sheet: 0.06 (0.19), residues: 663 loop : -1.55 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1019 TYR 0.028 0.002 TYR C 674 PHE 0.031 0.002 PHE A 172 TRP 0.009 0.001 TRP C 436 HIS 0.006 0.002 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (27585) covalent geometry : angle 0.65109 / 0.33 (37572) SS BOND : bond 0.00534 / 0.34 ( 39) SS BOND : angle 2.10131 / 1.54 ( 78) hydrogen bonds : bond 0.06591 / 4.27 ( 1015) hydrogen bonds : angle 5.59156 / 3.89 ( 2919) link_ALPHA1-2 : bond 0.00566 / 0.28 ( 3) link_ALPHA1-2 : angle 1.72359 / 0.78 ( 9) link_ALPHA1-3 : bond 0.01386 / 0.69 ( 3) link_ALPHA1-3 : angle 1.33998 / 0.64 ( 9) link_BETA1-4 : bond 0.00576 / 0.38 ( 66) link_BETA1-4 : angle 2.52161 / 1.77 ( 198) link_NAG-ASN : bond 0.00644 / 0.34 ( 63) link_NAG-ASN : angle 1.87960 / 1.27 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 490 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0350 (tmm) cc_final: -0.1404 (tmm) REVERT: A 164 LYS cc_start: 0.7893 (pttt) cc_final: 0.7617 (pptt) REVERT: A 309 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 424 LYS cc_start: 0.8164 (tppt) cc_final: 0.7886 (tppt) REVERT: A 512 VAL cc_start: 0.8769 (t) cc_final: 0.8503 (m) REVERT: A 1084 ASP cc_start: 0.7821 (t70) cc_final: 0.7526 (t0) REVERT: B 127 VAL cc_start: 0.8209 (t) cc_final: 0.7922 (m) REVERT: B 177 MET cc_start: 0.4466 (mmm) cc_final: 0.4026 (mmm) REVERT: B 424 LYS cc_start: 0.8241 (tppt) cc_final: 0.8013 (tppt) REVERT: B 1084 ASP cc_start: 0.7914 (t70) cc_final: 0.7630 (t0) REVERT: C 127 VAL cc_start: 0.8074 (t) cc_final: 0.7835 (m) REVERT: C 153 MET cc_start: 0.1057 (tmm) cc_final: 0.0589 (tmm) REVERT: C 359 SER cc_start: 0.7946 (p) cc_final: 0.7726 (t) REVERT: C 424 LYS cc_start: 0.8175 (tppt) cc_final: 0.7833 (tppt) REVERT: C 512 VAL cc_start: 0.8730 (t) cc_final: 0.8499 (m) REVERT: C 931 ILE cc_start: 0.8777 (mm) cc_final: 0.8534 (tp) outliers start: 57 outliers final: 29 residues processed: 519 average time/residue: 0.6066 time to fit residues: 367.7755 Evaluate side-chains 498 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 469 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 311 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 202 optimal weight: 0.1980 chunk 305 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 613 GLN A 755 GLN A1002 GLN B 49 HIS B 66 HIS B 935 GLN B 949 GLN C 49 HIS C 66 HIS C 437 ASN C 613 GLN C 949 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.179644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141004 restraints weight = 36834.692| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.33 r_work: 0.3731 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27759 Z= 0.147 Angle : 0.647 9.504 38055 Z= 0.319 Chirality : 0.046 0.302 4641 Planarity : 0.005 0.051 4650 Dihedral : 6.183 56.063 6227 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.42 % Allowed : 11.69 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.14), residues: 3183 helix: 2.08 (0.20), residues: 693 sheet: 0.23 (0.20), residues: 651 loop : -1.53 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1019 TYR 0.022 0.002 TYR B 265 PHE 0.027 0.002 PHE A 172 TRP 0.008 0.001 TRP C 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (27585) covalent geometry : angle 0.60954 / 0.31 (37572) SS BOND : bond 0.00515 / 0.36 ( 39) SS BOND : angle 1.95881 / 1.40 ( 78) hydrogen bonds : bond 0.06563 / 4.26 ( 1015) hydrogen bonds : angle 5.49699 / 3.82 ( 2919) link_ALPHA1-2 : bond 0.00653 / 0.33 ( 3) link_ALPHA1-2 : angle 1.38329 / 0.63 ( 9) link_ALPHA1-3 : bond 0.01299 / 0.65 ( 3) link_ALPHA1-3 : angle 1.61010 / 0.75 ( 9) link_BETA1-4 : bond 0.00558 / 0.37 ( 66) link_BETA1-4 : angle 2.12309 / 1.47 ( 198) link_NAG-ASN : bond 0.00517 / 0.31 ( 63) link_NAG-ASN : angle 1.95694 / 1.35 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 478 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0250 (tmm) cc_final: -0.1359 (tmm) REVERT: A 164 LYS cc_start: 0.7885 (pttt) cc_final: 0.7617 (pptt) REVERT: A 424 LYS cc_start: 0.8196 (tppt) cc_final: 0.7917 (tppt) REVERT: A 512 VAL cc_start: 0.8771 (t) cc_final: 0.8515 (m) REVERT: A 1084 ASP cc_start: 0.7792 (t70) cc_final: 0.7478 (t0) REVERT: B 96 GLU cc_start: 0.6207 (pt0) cc_final: 0.5777 (mt-10) REVERT: B 127 VAL cc_start: 0.8211 (t) cc_final: 0.7919 (m) REVERT: B 153 MET cc_start: 0.0492 (tmm) cc_final: -0.0336 (tmm) REVERT: B 177 MET cc_start: 0.4532 (mmm) cc_final: 0.4054 (mmm) REVERT: B 424 LYS cc_start: 0.8258 (tppt) cc_final: 0.8020 (tppt) REVERT: B 1084 ASP cc_start: 0.7927 (t70) cc_final: 0.7640 (t0) REVERT: C 127 VAL cc_start: 0.8070 (t) cc_final: 0.7827 (m) REVERT: C 153 MET cc_start: 0.1052 (tmm) cc_final: 0.0538 (tmm) REVERT: C 377 PHE cc_start: 0.8169 (t80) cc_final: 0.7956 (t80) REVERT: C 512 VAL cc_start: 0.8707 (t) cc_final: 0.8499 (m) REVERT: C 619 GLU cc_start: 0.7090 (mp0) cc_final: 0.6851 (mp0) REVERT: C 931 ILE cc_start: 0.8788 (mm) cc_final: 0.8555 (tp) outliers start: 68 outliers final: 47 residues processed: 509 average time/residue: 0.5810 time to fit residues: 347.0919 Evaluate side-chains 505 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 458 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 291 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 230 optimal weight: 0.0470 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN B 935 GLN B 949 GLN C 437 ASN C 755 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.179016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139864 restraints weight = 36609.954| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.47 r_work: 0.3708 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27759 Z= 0.153 Angle : 0.642 12.016 38055 Z= 0.321 Chirality : 0.046 0.291 4641 Planarity : 0.005 0.057 4650 Dihedral : 5.226 56.494 6227 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.52 % Allowed : 12.54 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3183 helix: 2.03 (0.20), residues: 693 sheet: 0.38 (0.21), residues: 618 loop : -1.53 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 355 TYR 0.022 0.002 TYR B 265 PHE 0.024 0.002 PHE A 172 TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (27585) covalent geometry : angle 0.61082 / 0.31 (37572) SS BOND : bond 0.00450 / 0.31 ( 39) SS BOND : angle 2.03372 / 1.45 ( 78) hydrogen bonds : bond 0.06741 / 4.38 ( 1015) hydrogen bonds : angle 5.44630 / 3.77 ( 2919) link_ALPHA1-2 : bond 0.00583 / 0.29 ( 3) link_ALPHA1-2 : angle 1.37934 / 0.63 ( 9) link_ALPHA1-3 : bond 0.01118 / 0.56 ( 3) link_ALPHA1-3 : angle 1.56137 / 0.73 ( 9) link_BETA1-4 : bond 0.00515 / 0.34 ( 66) link_BETA1-4 : angle 1.77816 / 1.22 ( 198) link_NAG-ASN : bond 0.00526 / 0.31 ( 63) link_NAG-ASN : angle 1.90813 / 1.33 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 474 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0218 (tmm) cc_final: -0.1323 (tmm) REVERT: A 164 LYS cc_start: 0.7940 (pttt) cc_final: 0.7676 (pptt) REVERT: A 424 LYS cc_start: 0.8227 (tppt) cc_final: 0.7945 (tppt) REVERT: A 512 VAL cc_start: 0.8775 (t) cc_final: 0.8529 (m) REVERT: A 819 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 1084 ASP cc_start: 0.7867 (t70) cc_final: 0.7541 (t0) REVERT: B 96 GLU cc_start: 0.6261 (pt0) cc_final: 0.5845 (mt-10) REVERT: B 127 VAL cc_start: 0.8196 (t) cc_final: 0.7922 (m) REVERT: B 153 MET cc_start: 0.0739 (tmm) cc_final: 0.0139 (tmm) REVERT: B 177 MET cc_start: 0.4588 (mmm) cc_final: 0.4086 (mmm) REVERT: B 424 LYS cc_start: 0.8271 (tppt) cc_final: 0.8026 (tppt) REVERT: B 1084 ASP cc_start: 0.7939 (t70) cc_final: 0.7653 (t0) REVERT: C 153 MET cc_start: 0.1066 (tmm) cc_final: 0.0552 (tmm) REVERT: C 377 PHE cc_start: 0.8233 (t80) cc_final: 0.8029 (t80) REVERT: C 551 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8315 (p) REVERT: C 619 GLU cc_start: 0.7081 (mp0) cc_final: 0.6841 (mp0) REVERT: C 790 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8113 (mmtm) REVERT: C 931 ILE cc_start: 0.8802 (mm) cc_final: 0.8565 (tp) outliers start: 71 outliers final: 47 residues processed: 502 average time/residue: 0.5899 time to fit residues: 346.7583 Evaluate side-chains 511 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 463 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 198 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 201 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 755 GLN B 321 GLN B 755 GLN B 762 GLN B 935 GLN B 949 GLN C 437 ASN C 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.177558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138018 restraints weight = 36542.766| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.26 r_work: 0.3695 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27759 Z= 0.181 Angle : 0.672 10.886 38055 Z= 0.338 Chirality : 0.047 0.272 4641 Planarity : 0.005 0.058 4650 Dihedral : 5.166 56.011 6227 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.09 % Allowed : 12.79 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.14), residues: 3183 helix: 1.90 (0.20), residues: 693 sheet: 0.38 (0.20), residues: 636 loop : -1.57 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1019 TYR 0.023 0.002 TYR B 265 PHE 0.020 0.002 PHE A 172 TRP 0.011 0.001 TRP B 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (27585) covalent geometry : angle 0.63879 / 0.33 (37572) SS BOND : bond 0.00495 / 0.33 ( 39) SS BOND : angle 2.26160 / 1.61 ( 78) hydrogen bonds : bond 0.07286 / 4.75 ( 1015) hydrogen bonds : angle 5.49654 / 3.81 ( 2919) link_ALPHA1-2 : bond 0.00576 / 0.29 ( 3) link_ALPHA1-2 : angle 1.36028 / 0.63 ( 9) link_ALPHA1-3 : bond 0.00966 / 0.49 ( 3) link_ALPHA1-3 : angle 1.44627 / 0.68 ( 9) link_BETA1-4 : bond 0.00512 / 0.34 ( 66) link_BETA1-4 : angle 1.64505 / 1.12 ( 198) link_NAG-ASN : bond 0.00464 / 0.30 ( 63) link_NAG-ASN : angle 2.14071 / 1.48 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 472 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0241 (tmm) cc_final: -0.1003 (tmm) REVERT: A 164 LYS cc_start: 0.7960 (pttt) cc_final: 0.7690 (pptt) REVERT: A 424 LYS cc_start: 0.8224 (tppt) cc_final: 0.7940 (tppt) REVERT: A 512 VAL cc_start: 0.8789 (t) cc_final: 0.8528 (m) REVERT: A 819 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 1084 ASP cc_start: 0.7801 (t70) cc_final: 0.7499 (t0) REVERT: B 153 MET cc_start: 0.0778 (tmm) cc_final: 0.0144 (tmm) REVERT: B 177 MET cc_start: 0.4652 (mmm) cc_final: 0.4169 (mmm) REVERT: B 424 LYS cc_start: 0.8229 (tppt) cc_final: 0.7983 (tppt) REVERT: B 1084 ASP cc_start: 0.7891 (t70) cc_final: 0.7598 (t0) REVERT: C 153 MET cc_start: 0.1091 (tmm) cc_final: 0.0139 (tmm) REVERT: C 619 GLU cc_start: 0.7091 (mp0) cc_final: 0.6849 (mp0) REVERT: C 790 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8115 (mmtm) REVERT: C 931 ILE cc_start: 0.8801 (mm) cc_final: 0.8556 (tp) outliers start: 87 outliers final: 62 residues processed: 514 average time/residue: 0.5657 time to fit residues: 342.2448 Evaluate side-chains 531 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 469 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 40 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 152 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 450 ASN A 755 GLN A 935 GLN B 321 GLN B 755 GLN B 762 GLN B 949 GLN C 218 GLN C 437 ASN C 949 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.176794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137355 restraints weight = 36291.368| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.38 r_work: 0.3678 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27759 Z= 0.201 Angle : 0.696 11.640 38055 Z= 0.352 Chirality : 0.048 0.301 4641 Planarity : 0.005 0.058 4650 Dihedral : 5.127 56.018 6227 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.95 % Allowed : 13.61 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.14), residues: 3183 helix: 1.80 (0.20), residues: 693 sheet: 0.26 (0.21), residues: 606 loop : -1.57 (0.12), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1019 TYR 0.024 0.002 TYR B 265 PHE 0.024 0.002 PHE B 172 TRP 0.010 0.001 TRP B 886 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (27585) covalent geometry : angle 0.66293 / 0.34 (37572) SS BOND : bond 0.00537 / 0.36 ( 39) SS BOND : angle 2.34855 / 1.67 ( 78) hydrogen bonds : bond 0.07633 / 4.98 ( 1015) hydrogen bonds : angle 5.55751 / 3.86 ( 2919) link_ALPHA1-2 : bond 0.00546 / 0.27 ( 3) link_ALPHA1-2 : angle 1.33303 / 0.63 ( 9) link_ALPHA1-3 : bond 0.01035 / 0.52 ( 3) link_ALPHA1-3 : angle 1.39307 / 0.66 ( 9) link_BETA1-4 : bond 0.00519 / 0.34 ( 66) link_BETA1-4 : angle 1.63865 / 1.09 ( 198) link_NAG-ASN : bond 0.00461 / 0.28 ( 63) link_NAG-ASN : angle 2.20940 / 1.54 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 479 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0145 (tmm) cc_final: -0.0934 (tmm) REVERT: A 164 LYS cc_start: 0.7878 (pttt) cc_final: 0.7573 (pptt) REVERT: A 177 MET cc_start: 0.4590 (mmm) cc_final: 0.4245 (mmm) REVERT: A 512 VAL cc_start: 0.8755 (t) cc_final: 0.8427 (m) REVERT: A 819 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 1084 ASP cc_start: 0.7385 (t70) cc_final: 0.7111 (t0) REVERT: B 153 MET cc_start: 0.0834 (tmm) cc_final: -0.0112 (tmm) REVERT: B 177 MET cc_start: 0.4547 (mmm) cc_final: 0.4091 (mmm) REVERT: B 324 GLU cc_start: 0.6411 (mp0) cc_final: 0.6200 (mp0) REVERT: B 424 LYS cc_start: 0.8101 (tppt) cc_final: 0.7855 (tppt) REVERT: B 1084 ASP cc_start: 0.7527 (t70) cc_final: 0.7266 (t0) REVERT: C 153 MET cc_start: 0.1008 (tmm) cc_final: 0.0054 (tmm) REVERT: C 660 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: C 790 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7907 (mmtm) REVERT: C 931 ILE cc_start: 0.8704 (mm) cc_final: 0.8440 (tp) outliers start: 83 outliers final: 68 residues processed: 515 average time/residue: 0.5696 time to fit residues: 344.1194 Evaluate side-chains 539 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 470 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 288 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 301 optimal weight: 0.0970 chunk 183 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 755 GLN B 321 GLN B 755 GLN B 762 GLN B 949 GLN C 437 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.177944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139392 restraints weight = 36586.660| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.53 r_work: 0.3699 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27759 Z= 0.157 Angle : 0.658 11.937 38055 Z= 0.332 Chirality : 0.046 0.291 4641 Planarity : 0.005 0.057 4650 Dihedral : 5.054 55.972 6227 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.81 % Allowed : 14.25 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.53 (0.14), residues: 3183 helix: 1.85 (0.20), residues: 693 sheet: 0.39 (0.21), residues: 633 loop : -1.58 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1019 TYR 0.023 0.002 TYR B 265 PHE 0.030 0.002 PHE B 172 TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (27585) covalent geometry : angle 0.62273 / 0.32 (37572) SS BOND : bond 0.00471 / 0.31 ( 39) SS BOND : angle 2.13393 / 1.51 ( 78) hydrogen bonds : bond 0.06943 / 4.53 ( 1015) hydrogen bonds : angle 5.44682 / 3.78 ( 2919) link_ALPHA1-2 : bond 0.00555 / 0.28 ( 3) link_ALPHA1-2 : angle 1.32829 / 0.62 ( 9) link_ALPHA1-3 : bond 0.00962 / 0.48 ( 3) link_ALPHA1-3 : angle 1.30025 / 0.61 ( 9) link_BETA1-4 : bond 0.00516 / 0.34 ( 66) link_BETA1-4 : angle 1.52833 / 1.03 ( 198) link_NAG-ASN : bond 0.00489 / 0.31 ( 63) link_NAG-ASN : angle 2.38906 / 1.67 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 470 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0228 (tmm) cc_final: -0.1346 (tmm) REVERT: A 164 LYS cc_start: 0.7943 (pttt) cc_final: 0.7641 (pptt) REVERT: A 177 MET cc_start: 0.4710 (mmm) cc_final: 0.4331 (mmm) REVERT: A 512 VAL cc_start: 0.8763 (t) cc_final: 0.8507 (m) REVERT: A 819 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 1084 ASP cc_start: 0.7807 (t70) cc_final: 0.7483 (t0) REVERT: B 153 MET cc_start: 0.0880 (tmm) cc_final: 0.0209 (tmm) REVERT: B 177 MET cc_start: 0.4688 (mmm) cc_final: 0.4181 (mmm) REVERT: B 324 GLU cc_start: 0.6685 (mp0) cc_final: 0.6381 (mp0) REVERT: B 424 LYS cc_start: 0.8262 (tppt) cc_final: 0.8020 (tppt) REVERT: B 900 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7899 (mtp) REVERT: B 1084 ASP cc_start: 0.7919 (t70) cc_final: 0.7629 (t0) REVERT: C 153 MET cc_start: 0.1092 (tmm) cc_final: 0.0136 (tmm) REVERT: C 377 PHE cc_start: 0.8252 (t80) cc_final: 0.8040 (t80) REVERT: C 551 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8318 (p) REVERT: C 790 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8131 (mmtm) REVERT: C 931 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8544 (tp) outliers start: 79 outliers final: 63 residues processed: 502 average time/residue: 0.5614 time to fit residues: 332.1596 Evaluate side-chains 529 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 463 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 55 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 314 optimal weight: 0.6980 chunk 176 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 755 GLN B 321 GLN B 450 ASN B 755 GLN B 762 GLN B 949 GLN C 437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.177907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138898 restraints weight = 36653.654| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.45 r_work: 0.3706 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27759 Z= 0.142 Angle : 0.644 12.413 38055 Z= 0.325 Chirality : 0.046 0.479 4641 Planarity : 0.005 0.058 4650 Dihedral : 5.001 55.954 6227 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.67 % Allowed : 14.82 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.45 (0.14), residues: 3183 helix: 1.90 (0.20), residues: 693 sheet: 0.46 (0.21), residues: 633 loop : -1.54 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1019 TYR 0.023 0.001 TYR A 265 PHE 0.030 0.001 PHE B 172 TRP 0.009 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (27585) covalent geometry : angle 0.60958 / 0.32 (37572) SS BOND : bond 0.00434 / 0.29 ( 39) SS BOND : angle 2.04337 / 1.44 ( 78) hydrogen bonds : bond 0.06542 / 4.25 ( 1015) hydrogen bonds : angle 5.36887 / 3.73 ( 2919) link_ALPHA1-2 : bond 0.00534 / 0.27 ( 3) link_ALPHA1-2 : angle 1.31737 / 0.62 ( 9) link_ALPHA1-3 : bond 0.00923 / 0.46 ( 3) link_ALPHA1-3 : angle 1.24465 / 0.60 ( 9) link_BETA1-4 : bond 0.00507 / 0.33 ( 66) link_BETA1-4 : angle 1.47223 / 1.00 ( 198) link_NAG-ASN : bond 0.00538 / 0.34 ( 63) link_NAG-ASN : angle 2.36296 / 1.63 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 470 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0246 (tmm) cc_final: -0.0991 (tmm) REVERT: A 164 LYS cc_start: 0.7961 (pttt) cc_final: 0.7647 (pptt) REVERT: A 177 MET cc_start: 0.4709 (mmm) cc_final: 0.4316 (mmm) REVERT: A 512 VAL cc_start: 0.8748 (t) cc_final: 0.8500 (m) REVERT: A 819 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 1084 ASP cc_start: 0.7798 (t70) cc_final: 0.7477 (t0) REVERT: B 95 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7056 (tt) REVERT: B 153 MET cc_start: 0.0970 (tmm) cc_final: 0.0288 (tmm) REVERT: B 177 MET cc_start: 0.4681 (mmm) cc_final: 0.4165 (mmm) REVERT: B 324 GLU cc_start: 0.6679 (mp0) cc_final: 0.6376 (mp0) REVERT: B 424 LYS cc_start: 0.8220 (tppt) cc_final: 0.7976 (tppt) REVERT: B 900 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7851 (mtp) REVERT: B 1084 ASP cc_start: 0.7900 (t70) cc_final: 0.7601 (t0) REVERT: C 153 MET cc_start: 0.1078 (tmm) cc_final: 0.0107 (tmm) REVERT: C 314 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: C 324 GLU cc_start: 0.6679 (mp0) cc_final: 0.6460 (mp0) REVERT: C 377 PHE cc_start: 0.8239 (t80) cc_final: 0.8036 (t80) REVERT: C 551 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8319 (p) REVERT: C 790 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8123 (mmtm) REVERT: C 931 ILE cc_start: 0.8787 (mm) cc_final: 0.8550 (tp) outliers start: 75 outliers final: 59 residues processed: 501 average time/residue: 0.5712 time to fit residues: 336.5931 Evaluate side-chains 527 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 464 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 61 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 184 optimal weight: 0.1980 chunk 165 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 163 optimal weight: 0.0030 chunk 109 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 755 GLN B 321 GLN B 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.178083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139050 restraints weight = 36611.898| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.36 r_work: 0.3704 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27759 Z= 0.141 Angle : 0.635 11.490 38055 Z= 0.320 Chirality : 0.046 0.314 4641 Planarity : 0.005 0.056 4650 Dihedral : 4.936 55.845 6227 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.31 % Allowed : 15.14 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.45 (0.14), residues: 3183 helix: 1.94 (0.20), residues: 690 sheet: 0.39 (0.20), residues: 666 loop : -1.54 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1019 TYR 0.022 0.001 TYR B 265 PHE 0.030 0.001 PHE B 592 TRP 0.009 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (27585) covalent geometry : angle 0.60173 / 0.31 (37572) SS BOND : bond 0.00423 / 0.28 ( 39) SS BOND : angle 1.95052 / 1.33 ( 78) hydrogen bonds : bond 0.06440 / 4.18 ( 1015) hydrogen bonds : angle 5.33082 / 3.70 ( 2919) link_ALPHA1-2 : bond 0.00527 / 0.26 ( 3) link_ALPHA1-2 : angle 1.33560 / 0.64 ( 9) link_ALPHA1-3 : bond 0.00862 / 0.43 ( 3) link_ALPHA1-3 : angle 1.22972 / 0.58 ( 9) link_BETA1-4 : bond 0.00507 / 0.33 ( 66) link_BETA1-4 : angle 1.43305 / 0.97 ( 198) link_NAG-ASN : bond 0.00474 / 0.28 ( 63) link_NAG-ASN : angle 2.33186 / 1.58 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 460 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0247 (tmm) cc_final: -0.0996 (tmm) REVERT: A 164 LYS cc_start: 0.7964 (pttt) cc_final: 0.7656 (pptt) REVERT: A 177 MET cc_start: 0.4729 (mmm) cc_final: 0.4340 (mmm) REVERT: A 512 VAL cc_start: 0.8719 (t) cc_final: 0.8475 (m) REVERT: A 819 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 1084 ASP cc_start: 0.7846 (t70) cc_final: 0.7524 (t0) REVERT: B 95 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7056 (tt) REVERT: B 153 MET cc_start: 0.0976 (tmm) cc_final: 0.0264 (tmm) REVERT: B 177 MET cc_start: 0.4707 (mmm) cc_final: 0.4186 (mmm) REVERT: B 324 GLU cc_start: 0.6650 (mp0) cc_final: 0.6307 (mp0) REVERT: B 424 LYS cc_start: 0.8221 (tppt) cc_final: 0.7975 (tppt) REVERT: B 900 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7846 (mtp) REVERT: B 1084 ASP cc_start: 0.7935 (t70) cc_final: 0.7635 (t0) REVERT: C 153 MET cc_start: 0.0983 (tmm) cc_final: 0.0002 (tmm) REVERT: C 324 GLU cc_start: 0.6697 (mp0) cc_final: 0.6449 (mp0) REVERT: C 377 PHE cc_start: 0.8251 (t80) cc_final: 0.8009 (t80) REVERT: C 551 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8325 (p) REVERT: C 790 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8138 (mmtm) REVERT: C 931 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8549 (tp) outliers start: 65 outliers final: 58 residues processed: 489 average time/residue: 0.5474 time to fit residues: 314.8808 Evaluate side-chains 515 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 453 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 265 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 291 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 269 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 184 optimal weight: 0.0670 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 0.0060 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN A 755 GLN B 321 GLN B 448 ASN B 949 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.179438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.141020 restraints weight = 36627.765| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.32 r_work: 0.3737 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27759 Z= 0.116 Angle : 0.604 13.344 38055 Z= 0.301 Chirality : 0.045 0.274 4641 Planarity : 0.005 0.056 4650 Dihedral : 4.810 55.797 6227 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.63 % Allowed : 15.92 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.30 (0.14), residues: 3183 helix: 2.08 (0.20), residues: 690 sheet: 0.46 (0.20), residues: 666 loop : -1.45 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.025 0.001 TYR B 674 PHE 0.030 0.001 PHE B 592 TRP 0.010 0.001 TRP B 452 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (27585) covalent geometry : angle 0.56990 / 0.29 (37572) SS BOND : bond 0.00360 / 0.23 ( 39) SS BOND : angle 1.58074 / 1.08 ( 78) hydrogen bonds : bond 0.05523 / 3.57 ( 1015) hydrogen bonds : angle 5.15871 / 3.59 ( 2919) link_ALPHA1-2 : bond 0.00517 / 0.26 ( 3) link_ALPHA1-2 : angle 1.35418 / 0.65 ( 9) link_ALPHA1-3 : bond 0.00795 / 0.40 ( 3) link_ALPHA1-3 : angle 1.22318 / 0.58 ( 9) link_BETA1-4 : bond 0.00514 / 0.33 ( 66) link_BETA1-4 : angle 1.37912 / 0.94 ( 198) link_NAG-ASN : bond 0.00426 / 0.25 ( 63) link_NAG-ASN : angle 2.40579 / 1.62 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14463.30 seconds wall clock time: 245 minutes 28.56 seconds (14728.56 seconds total)