Starting phenix.real_space_refine on Tue Mar 3 21:21:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wky_21813/03_2026/6wky_21813.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wky_21813/03_2026/6wky_21813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2026/6wky_21813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2026/6wky_21813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2026/6wky_21813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2026/6wky_21813.map" } resolution = 4.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 3 Type Number sf(0) Gaussians C 5800 2.51 5 N 1620 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 40 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "a" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "b" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "e" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "f" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "i" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "j" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "m" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "n" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "o" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "p" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "q" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "r" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "s" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "t" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Time building chain proxies: 2.25, per 1000 atoms: 0.25 Number of scatterers: 9140 At special positions: 0 Unit cell: (96.72, 96.72, 99.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1720 8.00 N 1620 7.00 C 5800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 317.0 milliseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 92.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 1 through 28 removed outlier: 3.890A pdb=" N TYR B 8 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 28 removed outlier: 3.726A pdb=" N TYR C 8 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 19 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 28 removed outlier: 3.832A pdb=" N TYR D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA D 9 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP D 15 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 19 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 28 removed outlier: 4.255A pdb=" N TYR A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.531A pdb=" N ARG E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR E 8 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 9 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP E 15 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 19 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 21 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU E 24 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 26 " --> pdb=" O HIS E 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 28 removed outlier: 3.961A pdb=" N TYR F 8 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA F 14 " --> pdb=" O ARG F 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 19 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU F 26 " --> pdb=" O HIS F 22 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 21 removed outlier: 3.726A pdb=" N TYR G 8 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP G 15 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 21 " --> pdb=" O LYS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'H' and resid 2 through 28 removed outlier: 3.605A pdb=" N ARG H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA H 14 " --> pdb=" O ARG H 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP H 15 " --> pdb=" O ILE H 11 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU H 26 " --> pdb=" O HIS H 22 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 28 removed outlier: 4.076A pdb=" N TYR I 8 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA I 9 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG I 10 " --> pdb=" O ARG I 6 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 14 " --> pdb=" O ARG I 10 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU I 19 " --> pdb=" O ASP I 15 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA I 21 " --> pdb=" O LYS I 17 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU I 24 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU I 26 " --> pdb=" O HIS I 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA I 28 " --> pdb=" O GLU I 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 28 removed outlier: 3.828A pdb=" N TYR J 8 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA J 9 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG J 10 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA J 14 " --> pdb=" O ARG J 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA J 16 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 19 " --> pdb=" O ASP J 15 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU J 26 " --> pdb=" O HIS J 22 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 28 removed outlier: 3.928A pdb=" N TYR K 8 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA K 9 " --> pdb=" O LEU K 5 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA K 14 " --> pdb=" O ARG K 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA K 16 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU K 19 " --> pdb=" O ASP K 15 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA K 21 " --> pdb=" O LYS K 17 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU K 26 " --> pdb=" O HIS K 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 28 removed outlier: 4.136A pdb=" N TYR L 8 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA L 9 " --> pdb=" O LEU L 5 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG L 10 " --> pdb=" O ARG L 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA L 14 " --> pdb=" O ARG L 10 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 19 " --> pdb=" O ASP L 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA L 21 " --> pdb=" O LYS L 17 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU L 26 " --> pdb=" O HIS L 22 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 28 " --> pdb=" O GLU L 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 28 removed outlier: 4.176A pdb=" N TYR M 8 " --> pdb=" O ILE M 4 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA M 9 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG M 10 " --> pdb=" O ARG M 6 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA M 14 " --> pdb=" O ARG M 10 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS M 17 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU M 19 " --> pdb=" O ASP M 15 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA M 21 " --> pdb=" O LYS M 17 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU M 26 " --> pdb=" O HIS M 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 28 removed outlier: 3.719A pdb=" N TYR N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG N 10 " --> pdb=" O ARG N 6 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA N 16 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS N 17 " --> pdb=" O GLU N 13 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU N 19 " --> pdb=" O ASP N 15 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA N 21 " --> pdb=" O LYS N 17 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU N 26 " --> pdb=" O HIS N 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 28 removed outlier: 3.962A pdb=" N TYR O 8 " --> pdb=" O ILE O 4 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA O 9 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG O 10 " --> pdb=" O ARG O 6 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA O 16 " --> pdb=" O LEU O 12 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS O 17 " --> pdb=" O GLU O 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU O 19 " --> pdb=" O ASP O 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU O 26 " --> pdb=" O HIS O 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 removed outlier: 4.251A pdb=" N TYR P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA P 9 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG P 10 " --> pdb=" O ARG P 6 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP P 15 " --> pdb=" O ILE P 11 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS P 17 " --> pdb=" O GLU P 13 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA P 21 " --> pdb=" O LYS P 17 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU P 26 " --> pdb=" O HIS P 22 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA P 28 " --> pdb=" O GLU P 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 28 removed outlier: 3.921A pdb=" N TYR Q 8 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Q 9 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA Q 16 " --> pdb=" O LEU Q 12 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS Q 17 " --> pdb=" O GLU Q 13 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU Q 19 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA Q 21 " --> pdb=" O LYS Q 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU Q 24 " --> pdb=" O GLU Q 20 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU Q 26 " --> pdb=" O HIS Q 22 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA Q 28 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 28 removed outlier: 3.687A pdb=" N TYR R 8 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA R 9 " --> pdb=" O LEU R 5 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG R 10 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA R 14 " --> pdb=" O ARG R 10 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP R 15 " --> pdb=" O ILE R 11 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA R 16 " --> pdb=" O LEU R 12 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS R 17 " --> pdb=" O GLU R 13 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU R 19 " --> pdb=" O ASP R 15 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA R 21 " --> pdb=" O LYS R 17 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU R 26 " --> pdb=" O HIS R 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 28 removed outlier: 3.889A pdb=" N TYR S 8 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA S 9 " --> pdb=" O LEU S 5 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG S 10 " --> pdb=" O ARG S 6 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA S 14 " --> pdb=" O ARG S 10 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP S 15 " --> pdb=" O ILE S 11 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS S 17 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU S 19 " --> pdb=" O ASP S 15 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA S 21 " --> pdb=" O LYS S 17 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU S 24 " --> pdb=" O GLU S 20 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU S 26 " --> pdb=" O HIS S 22 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA S 28 " --> pdb=" O GLU S 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 28 removed outlier: 4.146A pdb=" N TYR T 8 " --> pdb=" O ILE T 4 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA T 9 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA T 14 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP T 15 " --> pdb=" O ILE T 11 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA T 16 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU T 19 " --> pdb=" O ASP T 15 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA T 21 " --> pdb=" O LYS T 17 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU T 26 " --> pdb=" O HIS T 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA T 28 " --> pdb=" O GLU T 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 28 removed outlier: 3.893A pdb=" N TYR a 8 " --> pdb=" O ILE a 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA a 9 " --> pdb=" O LEU a 5 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG a 10 " --> pdb=" O ARG a 6 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA a 14 " --> pdb=" O ARG a 10 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS a 17 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU a 19 " --> pdb=" O ASP a 15 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA a 21 " --> pdb=" O LYS a 17 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU a 26 " --> pdb=" O HIS a 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 28 removed outlier: 3.703A pdb=" N TYR b 8 " --> pdb=" O ILE b 4 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA b 9 " --> pdb=" O LEU b 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG b 10 " --> pdb=" O ARG b 6 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA b 14 " --> pdb=" O ARG b 10 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA b 16 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU b 19 " --> pdb=" O ASP b 15 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA b 21 " --> pdb=" O LYS b 17 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU b 26 " --> pdb=" O HIS b 22 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA b 28 " --> pdb=" O GLU b 24 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 28 removed outlier: 3.947A pdb=" N TYR c 8 " --> pdb=" O ILE c 4 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA c 9 " --> pdb=" O LEU c 5 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG c 10 " --> pdb=" O ARG c 6 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA c 14 " --> pdb=" O ARG c 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA c 16 " --> pdb=" O LEU c 12 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU c 19 " --> pdb=" O ASP c 15 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA c 21 " --> pdb=" O LYS c 17 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU c 24 " --> pdb=" O GLU c 20 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU c 26 " --> pdb=" O HIS c 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 28 removed outlier: 4.090A pdb=" N TYR d 8 " --> pdb=" O ILE d 4 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA d 9 " --> pdb=" O LEU d 5 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG d 10 " --> pdb=" O ARG d 6 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA d 16 " --> pdb=" O LEU d 12 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS d 17 " --> pdb=" O GLU d 13 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU d 19 " --> pdb=" O ASP d 15 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA d 21 " --> pdb=" O LYS d 17 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU d 26 " --> pdb=" O HIS d 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA d 28 " --> pdb=" O GLU d 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 28 removed outlier: 3.755A pdb=" N TYR e 8 " --> pdb=" O ILE e 4 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA e 9 " --> pdb=" O LEU e 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG e 10 " --> pdb=" O ARG e 6 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA e 14 " --> pdb=" O ARG e 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA e 16 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS e 17 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU e 19 " --> pdb=" O ASP e 15 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA e 21 " --> pdb=" O LYS e 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU e 24 " --> pdb=" O GLU e 20 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU e 26 " --> pdb=" O HIS e 22 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA e 28 " --> pdb=" O GLU e 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 28 removed outlier: 3.662A pdb=" N TYR f 8 " --> pdb=" O ILE f 4 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA f 9 " --> pdb=" O LEU f 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG f 10 " --> pdb=" O ARG f 6 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP f 15 " --> pdb=" O ILE f 11 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA f 16 " --> pdb=" O LEU f 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS f 17 " --> pdb=" O GLU f 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA f 21 " --> pdb=" O LYS f 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU f 26 " --> pdb=" O HIS f 22 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA f 28 " --> pdb=" O GLU f 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 28 removed outlier: 3.840A pdb=" N TYR g 8 " --> pdb=" O ILE g 4 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA g 9 " --> pdb=" O LEU g 5 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG g 10 " --> pdb=" O ARG g 6 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA g 14 " --> pdb=" O ARG g 10 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA g 16 " --> pdb=" O LEU g 12 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU g 19 " --> pdb=" O ASP g 15 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA g 21 " --> pdb=" O LYS g 17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU g 24 " --> pdb=" O GLU g 20 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU g 26 " --> pdb=" O HIS g 22 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA g 28 " --> pdb=" O GLU g 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 28 removed outlier: 4.025A pdb=" N TYR h 8 " --> pdb=" O ILE h 4 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA h 9 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG h 10 " --> pdb=" O ARG h 6 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA h 14 " --> pdb=" O ARG h 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP h 15 " --> pdb=" O ILE h 11 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA h 16 " --> pdb=" O LEU h 12 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS h 17 " --> pdb=" O GLU h 13 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU h 19 " --> pdb=" O ASP h 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA h 21 " --> pdb=" O LYS h 17 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU h 26 " --> pdb=" O HIS h 22 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA h 28 " --> pdb=" O GLU h 24 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 28 removed outlier: 4.099A pdb=" N TYR i 8 " --> pdb=" O ILE i 4 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA i 9 " --> pdb=" O LEU i 5 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG i 10 " --> pdb=" O ARG i 6 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA i 14 " --> pdb=" O ARG i 10 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA i 16 " --> pdb=" O LEU i 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS i 17 " --> pdb=" O GLU i 13 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU i 19 " --> pdb=" O ASP i 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA i 21 " --> pdb=" O LYS i 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU i 24 " --> pdb=" O GLU i 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU i 26 " --> pdb=" O HIS i 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA i 28 " --> pdb=" O GLU i 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 28 removed outlier: 3.795A pdb=" N TYR j 8 " --> pdb=" O ILE j 4 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA j 9 " --> pdb=" O LEU j 5 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG j 10 " --> pdb=" O ARG j 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA j 14 " --> pdb=" O ARG j 10 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA j 16 " --> pdb=" O LEU j 12 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS j 17 " --> pdb=" O GLU j 13 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU j 19 " --> pdb=" O ASP j 15 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA j 21 " --> pdb=" O LYS j 17 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU j 26 " --> pdb=" O HIS j 22 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 28 removed outlier: 3.848A pdb=" N TYR k 8 " --> pdb=" O ILE k 4 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA k 9 " --> pdb=" O LEU k 5 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG k 10 " --> pdb=" O ARG k 6 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA k 14 " --> pdb=" O ARG k 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU k 19 " --> pdb=" O ASP k 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA k 21 " --> pdb=" O LYS k 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU k 24 " --> pdb=" O GLU k 20 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU k 26 " --> pdb=" O HIS k 22 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA k 28 " --> pdb=" O GLU k 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 28 removed outlier: 4.073A pdb=" N TYR l 8 " --> pdb=" O ILE l 4 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA l 9 " --> pdb=" O LEU l 5 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG l 10 " --> pdb=" O ARG l 6 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA l 14 " --> pdb=" O ARG l 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS l 17 " --> pdb=" O GLU l 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU l 19 " --> pdb=" O ASP l 15 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU l 26 " --> pdb=" O HIS l 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA l 28 " --> pdb=" O GLU l 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 28 removed outlier: 3.871A pdb=" N TYR m 8 " --> pdb=" O ILE m 4 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA m 9 " --> pdb=" O LEU m 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG m 10 " --> pdb=" O ARG m 6 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA m 14 " --> pdb=" O ARG m 10 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA m 16 " --> pdb=" O LEU m 12 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS m 17 " --> pdb=" O GLU m 13 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE m 18 " --> pdb=" O ALA m 14 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU m 19 " --> pdb=" O ASP m 15 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA m 21 " --> pdb=" O LYS m 17 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU m 24 " --> pdb=" O GLU m 20 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU m 26 " --> pdb=" O HIS m 22 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA m 28 " --> pdb=" O GLU m 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 28 removed outlier: 3.722A pdb=" N TYR n 8 " --> pdb=" O ILE n 4 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA n 9 " --> pdb=" O LEU n 5 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG n 10 " --> pdb=" O ARG n 6 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP n 15 " --> pdb=" O ILE n 11 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA n 16 " --> pdb=" O LEU n 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS n 17 " --> pdb=" O GLU n 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU n 19 " --> pdb=" O ASP n 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU n 26 " --> pdb=" O HIS n 22 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA n 28 " --> pdb=" O GLU n 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 23 removed outlier: 4.024A pdb=" N TYR o 8 " --> pdb=" O ILE o 4 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA o 9 " --> pdb=" O LEU o 5 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG o 10 " --> pdb=" O ARG o 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA o 16 " --> pdb=" O LEU o 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS o 17 " --> pdb=" O GLU o 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU o 19 " --> pdb=" O ASP o 15 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA o 21 " --> pdb=" O LYS o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 28 removed outlier: 3.616A pdb=" N ALA o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 28 removed outlier: 4.134A pdb=" N TYR p 8 " --> pdb=" O ILE p 4 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA p 9 " --> pdb=" O LEU p 5 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG p 10 " --> pdb=" O ARG p 6 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA p 14 " --> pdb=" O ARG p 10 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP p 15 " --> pdb=" O ILE p 11 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA p 16 " --> pdb=" O LEU p 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS p 17 " --> pdb=" O GLU p 13 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU p 19 " --> pdb=" O ASP p 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA p 21 " --> pdb=" O LYS p 17 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU p 26 " --> pdb=" O HIS p 22 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA p 28 " --> pdb=" O GLU p 24 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 23 removed outlier: 3.876A pdb=" N TYR q 8 " --> pdb=" O ILE q 4 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA q 9 " --> pdb=" O LEU q 5 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG q 10 " --> pdb=" O ARG q 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA q 14 " --> pdb=" O ARG q 10 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA q 16 " --> pdb=" O LEU q 12 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS q 17 " --> pdb=" O GLU q 13 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU q 19 " --> pdb=" O ASP q 15 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA q 21 " --> pdb=" O LYS q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 23 through 28 removed outlier: 3.789A pdb=" N ALA q 28 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 25 removed outlier: 3.749A pdb=" N TYR r 8 " --> pdb=" O ILE r 4 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA r 9 " --> pdb=" O LEU r 5 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG r 10 " --> pdb=" O ARG r 6 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA r 14 " --> pdb=" O ARG r 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA r 16 " --> pdb=" O LEU r 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS r 17 " --> pdb=" O GLU r 13 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU r 19 " --> pdb=" O ASP r 15 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA r 21 " --> pdb=" O LYS r 17 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 23 removed outlier: 3.857A pdb=" N TYR s 8 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA s 9 " --> pdb=" O LEU s 5 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA s 14 " --> pdb=" O ARG s 10 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA s 16 " --> pdb=" O LEU s 12 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU s 19 " --> pdb=" O ASP s 15 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 23 through 28 removed outlier: 3.788A pdb=" N ALA s 28 " --> pdb=" O GLU s 24 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 25 removed outlier: 3.956A pdb=" N TYR t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA t 9 " --> pdb=" O LEU t 5 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA t 14 " --> pdb=" O ARG t 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA t 16 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS t 17 " --> pdb=" O GLU t 13 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU t 19 " --> pdb=" O ASP t 15 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA t 21 " --> pdb=" O LYS t 17 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1443 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: 1.35 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1680 1.29 - 1.35: 1552 1.35 - 1.42: 368 1.42 - 1.48: 1223 1.48 - 1.54: 4357 Bond restraints: 9180 Sorted by residual: bond pdb=" CA ILE m 18 " pdb=" C ILE m 18 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.18e-02 7.18e+03 1.23e+00 bond pdb=" CA ILE o 18 " pdb=" C ILE o 18 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.18e-02 7.18e+03 1.11e+00 bond pdb=" CA ILE D 18 " pdb=" C ILE D 18 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.22e-02 6.72e+03 1.02e+00 bond pdb=" CA ILE c 18 " pdb=" C ILE c 18 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.22e-02 6.72e+03 9.97e-01 bond pdb=" CA ILE C 18 " pdb=" C ILE C 18 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.23e-02 6.61e+03 9.78e-01 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11813 1.55 - 3.10: 411 3.10 - 4.64: 73 4.64 - 6.19: 19 6.19 - 7.74: 4 Bond angle restraints: 12320 Sorted by residual: angle pdb=" CA LEU E 5 " pdb=" CB LEU E 5 " pdb=" CG LEU E 5 " ideal model delta sigma weight residual 116.30 108.56 7.74 3.50e+00 8.16e-02 4.89e+00 angle pdb=" N HIS B 22 " pdb=" CA HIS B 22 " pdb=" C HIS B 22 " ideal model delta sigma weight residual 113.18 110.77 2.41 1.21e+00 6.83e-01 3.97e+00 angle pdb=" N HIS D 22 " pdb=" CA HIS D 22 " pdb=" C HIS D 22 " ideal model delta sigma weight residual 113.18 110.81 2.37 1.21e+00 6.83e-01 3.83e+00 angle pdb=" NE ARG T 6 " pdb=" CZ ARG T 6 " pdb=" NH1 ARG T 6 " ideal model delta sigma weight residual 121.50 119.55 1.95 1.00e+00 1.00e+00 3.80e+00 angle pdb=" NE ARG p 6 " pdb=" CZ ARG p 6 " pdb=" NH1 ARG p 6 " ideal model delta sigma weight residual 121.50 119.56 1.94 1.00e+00 1.00e+00 3.77e+00 ... (remaining 12315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4993 17.99 - 35.98: 627 35.98 - 53.98: 137 53.98 - 71.97: 3 71.97 - 89.96: 20 Dihedral angle restraints: 5780 sinusoidal: 2340 harmonic: 3440 Sorted by residual: dihedral pdb=" CA ILE j 18 " pdb=" C ILE j 18 " pdb=" N LEU j 19 " pdb=" CA LEU j 19 " ideal model delta harmonic sigma weight residual 180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ILE h 18 " pdb=" C ILE h 18 " pdb=" N LEU h 19 " pdb=" CA LEU h 19 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE A 18 " pdb=" C ILE A 18 " pdb=" N LEU A 19 " pdb=" CA LEU A 19 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 5777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 696 0.035 - 0.069: 500 0.069 - 0.104: 219 0.104 - 0.138: 33 0.138 - 0.173: 12 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CB ILE a 25 " pdb=" CA ILE a 25 " pdb=" CG1 ILE a 25 " pdb=" CG2 ILE a 25 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB ILE c 25 " pdb=" CA ILE c 25 " pdb=" CG1 ILE c 25 " pdb=" CG2 ILE c 25 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CB ILE f 25 " pdb=" CA ILE f 25 " pdb=" CG1 ILE f 25 " pdb=" CG2 ILE f 25 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 1457 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE o 18 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE o 18 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE o 18 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU o 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE m 18 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C ILE m 18 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE m 18 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU m 19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 25 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C ILE O 25 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE O 25 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU O 26 " -0.008 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3063 2.87 - 3.38: 10129 3.38 - 3.89: 14243 3.89 - 4.39: 18928 4.39 - 4.90: 26990 Nonbonded interactions: 73353 Sorted by model distance: nonbonded pdb=" O LYS a 27 " pdb=" NH2 ARG h 10 " model vdw 2.366 3.120 nonbonded pdb=" O LYS c 27 " pdb=" NH2 ARG f 10 " model vdw 2.368 3.120 nonbonded pdb=" OE1 GLN M 29 " pdb=" NH1 ARG T 6 " model vdw 2.373 3.120 nonbonded pdb=" O LYS M 27 " pdb=" NH2 ARG d 10 " model vdw 2.377 3.120 nonbonded pdb=" O LYS f 27 " pdb=" NH2 ARG m 10 " model vdw 2.377 3.120 ... (remaining 73348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'B' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'I' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'J' selection = chain 'K' selection = (chain 'L' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'M' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'Q' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'R' selection = chain 'S' selection = (chain 'T' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'a' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'b' selection = chain 'c' selection = (chain 'd' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'e' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'f' selection = chain 'g' selection = (chain 'h' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'i' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'j' selection = chain 'k' selection = (chain 'l' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'm' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'n' selection = chain 'o' selection = (chain 'p' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = (chain 'q' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) selection = chain 'r' selection = chain 's' selection = (chain 't' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 29)) } 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 group one per residue 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.340 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 0.037 9180 Z= 0.326 Angle : 0.744 7.738 12320 Z= 0.434 Chirality : 0.051 0.173 1460 Planarity : 0.004 0.015 1600 Dihedral : 16.884 89.960 3500 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % 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: -5.20 (0.19), residues: 1080 helix: -4.07 (0.11), residues: 900 sheet: None (None), residues: 0 loop : 2.25 (0.22), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 10 TYR 0.005 0.001 TYR T 8 HIS 0.005 0.002 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 9180) covalent geometry : angle 0.74408 (12320) hydrogen bonds : bond 0.32430 ( 481) hydrogen bonds : angle 9.65941 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 0.352 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.9198 (tt0) cc_final: 0.8889 (tp30) REVERT: C 3 GLU cc_start: 0.9005 (tt0) cc_final: 0.8767 (tp30) REVERT: D 4 ILE cc_start: 0.9603 (mt) cc_final: 0.9321 (tt) REVERT: A 5 LEU cc_start: 0.9538 (mt) cc_final: 0.9122 (mt) REVERT: E 20 GLU cc_start: 0.8860 (pt0) cc_final: 0.8591 (pt0) REVERT: F 13 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8880 (mp0) REVERT: F 17 LYS cc_start: 0.9562 (mptt) cc_final: 0.9272 (mmtp) REVERT: H 11 ILE cc_start: 0.9443 (mt) cc_final: 0.9204 (mt) REVERT: H 13 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8837 (mp0) REVERT: H 17 LYS cc_start: 0.9566 (mptt) cc_final: 0.9277 (mmtp) REVERT: K 13 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8849 (mt-10) REVERT: K 27 LYS cc_start: 0.9444 (tptm) cc_final: 0.9242 (tptp) REVERT: L 17 LYS cc_start: 0.9481 (mptt) cc_final: 0.9255 (mmtt) REVERT: L 27 LYS cc_start: 0.9460 (tttt) cc_final: 0.9230 (tptp) REVERT: M 3 GLU cc_start: 0.8902 (tt0) cc_final: 0.8698 (tp30) REVERT: M 13 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8762 (mt-10) REVERT: P 3 GLU cc_start: 0.8963 (tt0) cc_final: 0.8758 (tp30) REVERT: P 26 LEU cc_start: 0.9198 (mp) cc_final: 0.8994 (mp) REVERT: Q 1 GLN cc_start: 0.8591 (mt0) cc_final: 0.8231 (tp-100) REVERT: Q 3 GLU cc_start: 0.9221 (tt0) cc_final: 0.8880 (tp30) REVERT: Q 5 LEU cc_start: 0.9415 (mt) cc_final: 0.8931 (mt) REVERT: R 3 GLU cc_start: 0.9137 (tt0) cc_final: 0.8840 (tp30) REVERT: S 4 ILE cc_start: 0.9590 (mt) cc_final: 0.9261 (tt) REVERT: S 20 GLU cc_start: 0.9061 (pt0) cc_final: 0.8758 (pt0) REVERT: S 27 LYS cc_start: 0.9339 (tptm) cc_final: 0.9135 (tptp) REVERT: a 3 GLU cc_start: 0.9231 (tt0) cc_final: 0.8972 (tp30) REVERT: a 13 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8844 (mp0) REVERT: a 17 LYS cc_start: 0.9576 (mptt) cc_final: 0.9049 (mmtt) REVERT: b 17 LYS cc_start: 0.9442 (mptt) cc_final: 0.9169 (mmtt) REVERT: b 27 LYS cc_start: 0.9525 (tttt) cc_final: 0.9242 (tptp) REVERT: d 17 LYS cc_start: 0.9455 (mptt) cc_final: 0.9185 (mmtt) REVERT: e 3 GLU cc_start: 0.9172 (tt0) cc_final: 0.8886 (tp30) REVERT: e 20 GLU cc_start: 0.8997 (pt0) cc_final: 0.8659 (pt0) REVERT: e 27 LYS cc_start: 0.9512 (tptm) cc_final: 0.9210 (tptp) REVERT: f 3 GLU cc_start: 0.9107 (tt0) cc_final: 0.8749 (tp30) REVERT: g 20 GLU cc_start: 0.8998 (pt0) cc_final: 0.8654 (pt0) REVERT: g 27 LYS cc_start: 0.9508 (tptm) cc_final: 0.9210 (tptp) REVERT: h 1 GLN cc_start: 0.8525 (mt0) cc_final: 0.8155 (tp-100) REVERT: h 5 LEU cc_start: 0.9355 (mt) cc_final: 0.9101 (mt) REVERT: h 11 ILE cc_start: 0.9317 (mt) cc_final: 0.9093 (mt) REVERT: i 13 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8917 (mp0) REVERT: i 17 LYS cc_start: 0.9583 (mptt) cc_final: 0.9321 (mmtt) REVERT: j 17 LYS cc_start: 0.9579 (mptt) cc_final: 0.9238 (mmtm) REVERT: k 13 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8831 (mp0) REVERT: k 17 LYS cc_start: 0.9583 (mptt) cc_final: 0.9331 (mmtt) REVERT: m 3 GLU cc_start: 0.9037 (tt0) cc_final: 0.8805 (tp30) REVERT: m 13 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8670 (mp0) REVERT: m 17 LYS cc_start: 0.9589 (mptt) cc_final: 0.9170 (mmtm) REVERT: n 3 GLU cc_start: 0.9026 (tt0) cc_final: 0.8782 (tp30) REVERT: o 13 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8648 (mp0) REVERT: o 17 LYS cc_start: 0.9598 (mptt) cc_final: 0.9133 (mmtm) REVERT: o 20 GLU cc_start: 0.8843 (pt0) cc_final: 0.8457 (pt0) REVERT: o 29 GLN cc_start: 0.8330 (tt0) cc_final: 0.7509 (tt0) REVERT: p 3 GLU cc_start: 0.9049 (tt0) cc_final: 0.8791 (tp30) REVERT: q 1 GLN cc_start: 0.8159 (mt0) cc_final: 0.7832 (tp40) REVERT: q 3 GLU cc_start: 0.9063 (tt0) cc_final: 0.8591 (tp30) REVERT: q 5 LEU cc_start: 0.8875 (mp) cc_final: 0.8394 (mp) REVERT: q 13 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8705 (mp0) REVERT: q 17 LYS cc_start: 0.9656 (mptt) cc_final: 0.9301 (mmtt) REVERT: q 24 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9188 (mm-30) REVERT: r 3 GLU cc_start: 0.9238 (tt0) cc_final: 0.8613 (tp30) REVERT: r 17 LYS cc_start: 0.9601 (mptt) cc_final: 0.9124 (mmtt) REVERT: r 24 GLU cc_start: 0.9351 (tp30) cc_final: 0.9045 (tm-30) REVERT: r 26 LEU cc_start: 0.8981 (mp) cc_final: 0.8520 (tp) REVERT: s 17 LYS cc_start: 0.9645 (mptt) cc_final: 0.9318 (mmtt) REVERT: s 24 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9181 (mm-30) REVERT: t 3 GLU cc_start: 0.9103 (tt0) cc_final: 0.8757 (tp30) REVERT: t 17 LYS cc_start: 0.9570 (mptt) cc_final: 0.9148 (mmtt) REVERT: t 24 GLU cc_start: 0.9393 (tp30) cc_final: 0.8981 (tm-30) REVERT: t 26 LEU cc_start: 0.9016 (mp) cc_final: 0.8555 (tp) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 0.0966 time to fit residues: 79.5364 Evaluate side-chains 317 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0030 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN R 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036547 restraints weight = 56522.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.037827 restraints weight = 29051.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038666 restraints weight = 17746.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039274 restraints weight = 12214.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.039721 restraints weight = 8877.243| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9180 Z= 0.151 Angle : 0.619 4.968 12320 Z= 0.351 Chirality : 0.039 0.120 1460 Planarity : 0.003 0.028 1600 Dihedral : 5.598 35.642 1280 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.93 % Allowed : 6.10 % Favored : 90.98 % 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: -5.06 (0.19), residues: 1080 helix: -2.98 (0.12), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 10 TYR 0.007 0.001 TYR a 8 HIS 0.003 0.001 HIS j 22 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9180) covalent geometry : angle 0.61862 (12320) hydrogen bonds : bond 0.05177 ( 481) hydrogen bonds : angle 6.22083 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 582 time to evaluate : 0.338 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN o 1 " (corrupted residue). Skipping it. 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: D 13 GLU cc_start: 0.9211 (tt0) cc_final: 0.8957 (mt-10) REVERT: A 17 LYS cc_start: 0.9547 (mptt) cc_final: 0.9029 (mmtm) REVERT: E 1 GLN cc_start: 0.7072 (tp40) cc_final: 0.6551 (tp-100) REVERT: E 17 LYS cc_start: 0.9436 (mptt) cc_final: 0.9224 (mmtp) REVERT: F 13 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8433 (mp0) REVERT: F 17 LYS cc_start: 0.9442 (mptt) cc_final: 0.9081 (mmtt) REVERT: F 20 GLU cc_start: 0.9141 (pp20) cc_final: 0.8819 (pp20) REVERT: H 1 GLN cc_start: 0.7366 (tp40) cc_final: 0.7112 (tp40) REVERT: H 20 GLU cc_start: 0.9140 (pp20) cc_final: 0.8796 (pp20) REVERT: I 5 LEU cc_start: 0.9694 (mt) cc_final: 0.9484 (mt) REVERT: I 13 GLU cc_start: 0.9401 (mt-10) cc_final: 0.8837 (mt-10) REVERT: K 13 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8989 (mp0) REVERT: L 1 GLN cc_start: 0.7058 (tp40) cc_final: 0.6687 (tp40) REVERT: L 5 LEU cc_start: 0.9695 (mt) cc_final: 0.9426 (mt) REVERT: L 13 GLU cc_start: 0.9024 (mp0) cc_final: 0.8808 (mp0) REVERT: L 17 LYS cc_start: 0.9414 (mptt) cc_final: 0.8912 (mmtm) REVERT: M 5 LEU cc_start: 0.9764 (mt) cc_final: 0.9257 (mp) REVERT: O 17 LYS cc_start: 0.9530 (mptt) cc_final: 0.9022 (mmtm) REVERT: P 17 LYS cc_start: 0.9596 (mptt) cc_final: 0.9043 (mmtm) REVERT: Q 17 LYS cc_start: 0.9436 (mptt) cc_final: 0.9010 (mmtt) REVERT: e 3 GLU cc_start: 0.9045 (tt0) cc_final: 0.8704 (tp30) REVERT: e 17 LYS cc_start: 0.9382 (mptt) cc_final: 0.8974 (mmtt) REVERT: e 27 LYS cc_start: 0.9359 (tptm) cc_final: 0.9108 (mmmt) REVERT: f 11 ILE cc_start: 0.9345 (mt) cc_final: 0.9066 (mt) REVERT: g 27 LYS cc_start: 0.9355 (tptm) cc_final: 0.9061 (mmmt) REVERT: h 5 LEU cc_start: 0.9462 (mt) cc_final: 0.9212 (mt) REVERT: i 13 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8799 (tm-30) REVERT: l 1 GLN cc_start: 0.6823 (tp40) cc_final: 0.6574 (tp40) REVERT: l 5 LEU cc_start: 0.9757 (mt) cc_final: 0.9519 (mt) REVERT: m 3 GLU cc_start: 0.8969 (tt0) cc_final: 0.8746 (tp30) REVERT: n 3 GLU cc_start: 0.8970 (tt0) cc_final: 0.8751 (tp30) REVERT: o 13 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8685 (mt-10) REVERT: p 1 GLN cc_start: 0.7371 (tp40) cc_final: 0.7115 (tp40) REVERT: q 13 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8522 (mt-10) REVERT: r 3 GLU cc_start: 0.8762 (tt0) cc_final: 0.8520 (tp30) REVERT: r 17 LYS cc_start: 0.9513 (mptt) cc_final: 0.9111 (mmtt) REVERT: r 20 GLU cc_start: 0.9222 (pp20) cc_final: 0.9021 (pp20) REVERT: r 26 LEU cc_start: 0.9068 (mp) cc_final: 0.8531 (tp) REVERT: t 17 LYS cc_start: 0.9486 (mptt) cc_final: 0.9087 (mmtt) REVERT: t 26 LEU cc_start: 0.8981 (mp) cc_final: 0.8507 (tp) outliers start: 24 outliers final: 0 residues processed: 582 average time/residue: 0.0991 time to fit residues: 78.4260 Evaluate side-chains 302 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035609 restraints weight = 60569.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.036832 restraints weight = 30627.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.037670 restraints weight = 18767.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.038245 restraints weight = 12748.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.038678 restraints weight = 9371.808| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9180 Z= 0.218 Angle : 0.658 5.455 12320 Z= 0.385 Chirality : 0.042 0.128 1460 Planarity : 0.004 0.041 1600 Dihedral : 5.793 37.062 1280 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.98 % Allowed : 5.12 % Favored : 93.90 % 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: -3.96 (0.20), residues: 1080 helix: -2.30 (0.12), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG f 10 TYR 0.009 0.001 TYR f 8 HIS 0.003 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9180) covalent geometry : angle 0.65846 (12320) hydrogen bonds : bond 0.04512 ( 481) hydrogen bonds : angle 6.34530 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 537 time to evaluate : 0.374 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. 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: 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: 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: B 1 GLN cc_start: 0.7554 (tp40) cc_final: 0.7141 (tp-100) REVERT: B 13 GLU cc_start: 0.9318 (tt0) cc_final: 0.8852 (mt-10) REVERT: C 17 LYS cc_start: 0.9551 (mptt) cc_final: 0.9102 (mmtm) REVERT: A 1 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7150 (tp-100) REVERT: F 20 GLU cc_start: 0.9162 (pp20) cc_final: 0.8859 (pp20) REVERT: H 1 GLN cc_start: 0.7275 (tp40) cc_final: 0.6909 (tp-100) REVERT: H 20 GLU cc_start: 0.9200 (pp20) cc_final: 0.8891 (pp20) REVERT: J 13 GLU cc_start: 0.9056 (mp0) cc_final: 0.8776 (mp0) REVERT: J 17 LYS cc_start: 0.9482 (mptt) cc_final: 0.9102 (mmtp) REVERT: K 13 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9060 (mp0) REVERT: L 1 GLN cc_start: 0.7207 (tp40) cc_final: 0.6867 (tp40) REVERT: L 5 LEU cc_start: 0.9693 (mt) cc_final: 0.9417 (mt) REVERT: O 13 GLU cc_start: 0.8905 (mp0) cc_final: 0.8614 (mp0) REVERT: O 17 LYS cc_start: 0.9486 (mptt) cc_final: 0.8990 (mmtt) REVERT: P 20 GLU cc_start: 0.9091 (pp20) cc_final: 0.8890 (pp20) REVERT: Q 1 GLN cc_start: 0.7144 (tp40) cc_final: 0.6832 (tp-100) REVERT: Q 5 LEU cc_start: 0.9695 (mt) cc_final: 0.9326 (mt) REVERT: R 20 GLU cc_start: 0.9071 (pp20) cc_final: 0.8839 (pp20) REVERT: S 17 LYS cc_start: 0.9525 (mptt) cc_final: 0.9125 (mmtt) REVERT: T 20 GLU cc_start: 0.9067 (pp20) cc_final: 0.8803 (pp20) REVERT: a 3 GLU cc_start: 0.8999 (pm20) cc_final: 0.8767 (pm20) REVERT: a 17 LYS cc_start: 0.9495 (mptt) cc_final: 0.9000 (mmtp) REVERT: e 17 LYS cc_start: 0.9376 (mptt) cc_final: 0.8878 (mmtt) REVERT: e 27 LYS cc_start: 0.9380 (tptm) cc_final: 0.9109 (mmmt) REVERT: g 27 LYS cc_start: 0.9372 (tptm) cc_final: 0.9128 (mmmt) REVERT: h 5 LEU cc_start: 0.9638 (mt) cc_final: 0.9298 (mt) REVERT: h 20 GLU cc_start: 0.9128 (pp20) cc_final: 0.8851 (pp20) REVERT: i 1 GLN cc_start: 0.7357 (tp-100) cc_final: 0.6865 (tp-100) REVERT: i 5 LEU cc_start: 0.9656 (mt) cc_final: 0.9442 (mt) REVERT: l 5 LEU cc_start: 0.9753 (mt) cc_final: 0.9485 (mt) REVERT: m 3 GLU cc_start: 0.9020 (tt0) cc_final: 0.8807 (tp30) REVERT: n 3 GLU cc_start: 0.8973 (tt0) cc_final: 0.8772 (tp30) REVERT: n 20 GLU cc_start: 0.9055 (pp20) cc_final: 0.8818 (pp20) REVERT: o 11 ILE cc_start: 0.9455 (mt) cc_final: 0.9130 (mt) REVERT: p 18 ILE cc_start: 0.9428 (mt) cc_final: 0.9224 (mt) REVERT: p 20 GLU cc_start: 0.9046 (pp20) cc_final: 0.8803 (pp20) REVERT: q 1 GLN cc_start: 0.7532 (tp40) cc_final: 0.7287 (tp40) REVERT: q 3 GLU cc_start: 0.9105 (pm20) cc_final: 0.8894 (pm20) REVERT: q 5 LEU cc_start: 0.9331 (mp) cc_final: 0.9115 (mp) REVERT: r 3 GLU cc_start: 0.8720 (tt0) cc_final: 0.8515 (tp30) REVERT: r 17 LYS cc_start: 0.9488 (mptt) cc_final: 0.9094 (mmtt) REVERT: r 20 GLU cc_start: 0.9142 (pp20) cc_final: 0.8888 (pp20) REVERT: r 24 GLU cc_start: 0.9265 (tp30) cc_final: 0.8908 (tm-30) REVERT: r 26 LEU cc_start: 0.9136 (mp) cc_final: 0.8693 (tp) REVERT: t 17 LYS cc_start: 0.9498 (mptt) cc_final: 0.9102 (mmtt) REVERT: t 20 GLU cc_start: 0.9079 (pp20) cc_final: 0.8850 (pp20) REVERT: t 24 GLU cc_start: 0.9269 (tp30) cc_final: 0.8913 (tm-30) REVERT: t 26 LEU cc_start: 0.9123 (mp) cc_final: 0.8705 (tp) outliers start: 8 outliers final: 0 residues processed: 537 average time/residue: 0.0980 time to fit residues: 71.2651 Evaluate side-chains 273 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.044508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.039064 restraints weight = 55819.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.040434 restraints weight = 27853.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041345 restraints weight = 16720.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041942 restraints weight = 11311.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.042419 restraints weight = 8422.026| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9180 Z= 0.126 Angle : 0.585 4.489 12320 Z= 0.333 Chirality : 0.038 0.122 1460 Planarity : 0.003 0.034 1600 Dihedral : 5.604 35.053 1280 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.85 % Allowed : 4.51 % Favored : 94.63 % 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: -2.81 (0.22), residues: 1080 helix: -1.59 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 10 TYR 0.007 0.001 TYR Q 8 HIS 0.001 0.000 HIS O 22 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9180) covalent geometry : angle 0.58477 (12320) hydrogen bonds : bond 0.03929 ( 481) hydrogen bonds : angle 5.30730 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 556 time to evaluate : 0.357 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: 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 TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 LYS cc_start: 0.9493 (mptt) cc_final: 0.9029 (mmtp) REVERT: A 20 GLU cc_start: 0.9107 (pp20) cc_final: 0.8890 (pp20) REVERT: E 1 GLN cc_start: 0.7427 (tp40) cc_final: 0.6967 (tp-100) REVERT: H 1 GLN cc_start: 0.7277 (tp40) cc_final: 0.6842 (tp-100) REVERT: O 13 GLU cc_start: 0.8968 (mp0) cc_final: 0.8662 (mp0) REVERT: O 17 LYS cc_start: 0.9462 (mptt) cc_final: 0.8985 (mmtt) REVERT: P 17 LYS cc_start: 0.9469 (mptt) cc_final: 0.8996 (mmtt) REVERT: P 20 GLU cc_start: 0.9051 (pp20) cc_final: 0.8836 (pp20) REVERT: Q 5 LEU cc_start: 0.9599 (mt) cc_final: 0.9376 (mt) REVERT: Q 17 LYS cc_start: 0.9426 (mptt) cc_final: 0.9123 (mmtt) REVERT: R 20 GLU cc_start: 0.9053 (pp20) cc_final: 0.8802 (pp20) REVERT: S 17 LYS cc_start: 0.9511 (mptt) cc_final: 0.9109 (mmtt) REVERT: a 3 GLU cc_start: 0.9151 (pm20) cc_final: 0.8893 (pm20) REVERT: b 17 LYS cc_start: 0.9412 (mptt) cc_final: 0.9082 (mmtt) REVERT: d 13 GLU cc_start: 0.9084 (mp0) cc_final: 0.8771 (mp0) REVERT: d 17 LYS cc_start: 0.9427 (mptt) cc_final: 0.9175 (mmtt) REVERT: e 17 LYS cc_start: 0.9410 (mptt) cc_final: 0.9061 (mmtt) REVERT: f 13 GLU cc_start: 0.8989 (mp0) cc_final: 0.8781 (mp0) REVERT: f 17 LYS cc_start: 0.9552 (mptt) cc_final: 0.9167 (mmtt) REVERT: h 5 LEU cc_start: 0.9578 (mt) cc_final: 0.9355 (mt) REVERT: h 17 LYS cc_start: 0.9391 (mptt) cc_final: 0.9013 (mmtt) REVERT: i 13 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8834 (tm-30) REVERT: i 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.8843 (mmmm) REVERT: k 13 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8853 (tm-30) REVERT: k 17 LYS cc_start: 0.9478 (mptt) cc_final: 0.9170 (mmmm) REVERT: k 20 GLU cc_start: 0.8922 (pm20) cc_final: 0.8709 (pm20) REVERT: l 17 LYS cc_start: 0.9501 (mptt) cc_final: 0.9191 (mmtp) REVERT: m 3 GLU cc_start: 0.8916 (tt0) cc_final: 0.8674 (tp30) REVERT: m 11 ILE cc_start: 0.9279 (mt) cc_final: 0.9001 (pt) REVERT: n 3 GLU cc_start: 0.8790 (tt0) cc_final: 0.8520 (tp30) REVERT: n 20 GLU cc_start: 0.9069 (pp20) cc_final: 0.8805 (pp20) REVERT: p 20 GLU cc_start: 0.9043 (pp20) cc_final: 0.8826 (pp20) REVERT: q 3 GLU cc_start: 0.9106 (pm20) cc_final: 0.8866 (pm20) REVERT: q 18 ILE cc_start: 0.9268 (mp) cc_final: 0.9053 (mp) REVERT: r 3 GLU cc_start: 0.8649 (tt0) cc_final: 0.8273 (tp30) REVERT: r 17 LYS cc_start: 0.9482 (mptt) cc_final: 0.9094 (mmtt) REVERT: r 20 GLU cc_start: 0.9060 (pp20) cc_final: 0.8802 (pp20) REVERT: r 24 GLU cc_start: 0.9253 (tp30) cc_final: 0.8968 (tm-30) REVERT: r 26 LEU cc_start: 0.9007 (mp) cc_final: 0.8624 (tp) REVERT: t 1 GLN cc_start: 0.8477 (mt0) cc_final: 0.8087 (tp-100) REVERT: t 5 LEU cc_start: 0.9425 (mt) cc_final: 0.9185 (mt) REVERT: t 13 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8742 (mp0) REVERT: t 17 LYS cc_start: 0.9482 (mptt) cc_final: 0.9128 (mmtt) REVERT: t 20 GLU cc_start: 0.8965 (pp20) cc_final: 0.8722 (pp20) REVERT: t 24 GLU cc_start: 0.9210 (tp30) cc_final: 0.8889 (tm-30) REVERT: t 26 LEU cc_start: 0.8980 (mp) cc_final: 0.8608 (tp) outliers start: 7 outliers final: 1 residues processed: 556 average time/residue: 0.0960 time to fit residues: 72.5822 Evaluate side-chains 299 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036809 restraints weight = 59412.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.038057 restraints weight = 29688.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038900 restraints weight = 17931.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039486 restraints weight = 12107.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.039903 restraints weight = 8777.136| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9180 Z= 0.182 Angle : 0.650 5.108 12320 Z= 0.378 Chirality : 0.041 0.142 1460 Planarity : 0.003 0.030 1600 Dihedral : 5.562 37.262 1280 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.73 % Allowed : 3.66 % Favored : 95.61 % 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: -2.43 (0.22), residues: 1080 helix: -1.36 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 10 TYR 0.007 0.001 TYR P 8 HIS 0.002 0.001 HIS r 22 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9180) covalent geometry : angle 0.64983 (12320) hydrogen bonds : bond 0.04056 ( 481) hydrogen bonds : angle 5.79247 ( 1443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 520 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.9559 (m-30) cc_final: 0.9336 (m-30) REVERT: B 17 LYS cc_start: 0.9447 (mptt) cc_final: 0.8947 (mmtp) REVERT: C 17 LYS cc_start: 0.9591 (mptt) cc_final: 0.9216 (mmtm) REVERT: D 17 LYS cc_start: 0.9471 (mptt) cc_final: 0.8980 (mmtt) REVERT: D 20 GLU cc_start: 0.8936 (pp20) cc_final: 0.8711 (pp20) REVERT: E 1 GLN cc_start: 0.7568 (tp40) cc_final: 0.7251 (tp-100) REVERT: E 17 LYS cc_start: 0.9390 (mptt) cc_final: 0.8983 (mmtp) REVERT: E 20 GLU cc_start: 0.9081 (pp20) cc_final: 0.8861 (pp20) REVERT: F 20 GLU cc_start: 0.9075 (pp20) cc_final: 0.8837 (pp20) REVERT: H 1 GLN cc_start: 0.7241 (tp40) cc_final: 0.7033 (tp40) REVERT: H 20 GLU cc_start: 0.9148 (pp20) cc_final: 0.8860 (pp20) REVERT: L 1 GLN cc_start: 0.7209 (tp40) cc_final: 0.6659 (tp-100) REVERT: L 5 LEU cc_start: 0.9714 (mt) cc_final: 0.9510 (mt) REVERT: O 13 GLU cc_start: 0.8842 (mp0) cc_final: 0.8615 (mt-10) REVERT: O 17 LYS cc_start: 0.9494 (mptt) cc_final: 0.9000 (mmtm) REVERT: P 17 LYS cc_start: 0.9452 (mptt) cc_final: 0.8897 (mmtt) REVERT: P 20 GLU cc_start: 0.8982 (pp20) cc_final: 0.8730 (pp20) REVERT: a 1 GLN cc_start: 0.8050 (tp40) cc_final: 0.7650 (tp40) REVERT: b 17 LYS cc_start: 0.9442 (mptt) cc_final: 0.9113 (mmtm) REVERT: d 13 GLU cc_start: 0.9132 (mp0) cc_final: 0.8899 (mp0) REVERT: d 17 LYS cc_start: 0.9528 (mptt) cc_final: 0.9038 (mmtt) REVERT: f 29 GLN cc_start: 0.8687 (mt0) cc_final: 0.8470 (mt0) REVERT: g 17 LYS cc_start: 0.9432 (mptt) cc_final: 0.8919 (mmtp) REVERT: h 5 LEU cc_start: 0.9626 (mt) cc_final: 0.9389 (mt) REVERT: h 17 LYS cc_start: 0.9431 (mptt) cc_final: 0.8902 (mmtp) REVERT: h 20 GLU cc_start: 0.9149 (pp20) cc_final: 0.8842 (pp20) REVERT: i 13 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8743 (tm-30) REVERT: i 17 LYS cc_start: 0.9484 (mptt) cc_final: 0.8730 (mmmm) REVERT: k 13 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8819 (tm-30) REVERT: k 17 LYS cc_start: 0.9477 (mptt) cc_final: 0.8729 (mmmm) REVERT: l 1 GLN cc_start: 0.7274 (tp40) cc_final: 0.6873 (tp40) REVERT: n 17 LYS cc_start: 0.9444 (mptt) cc_final: 0.8935 (mmtm) REVERT: n 20 GLU cc_start: 0.8884 (pp20) cc_final: 0.8614 (pp20) REVERT: o 11 ILE cc_start: 0.9447 (mt) cc_final: 0.9076 (mt) REVERT: o 12 LEU cc_start: 0.9514 (mm) cc_final: 0.9255 (mm) REVERT: o 17 LYS cc_start: 0.9491 (mptt) cc_final: 0.9077 (mmmm) REVERT: q 3 GLU cc_start: 0.9085 (pm20) cc_final: 0.8881 (pm20) REVERT: r 4 ILE cc_start: 0.9608 (mt) cc_final: 0.8933 (mt) REVERT: r 17 LYS cc_start: 0.9486 (mptt) cc_final: 0.9084 (mmtt) REVERT: r 20 GLU cc_start: 0.9136 (pp20) cc_final: 0.8861 (pp20) REVERT: r 24 GLU cc_start: 0.9283 (tp30) cc_final: 0.8993 (tm-30) REVERT: r 26 LEU cc_start: 0.9055 (mp) cc_final: 0.8689 (tp) REVERT: t 1 GLN cc_start: 0.8540 (mt0) cc_final: 0.8211 (tp-100) REVERT: t 5 LEU cc_start: 0.9417 (mt) cc_final: 0.9167 (mt) REVERT: t 17 LYS cc_start: 0.9487 (mptt) cc_final: 0.9058 (mmtt) REVERT: t 24 GLU cc_start: 0.9313 (tp30) cc_final: 0.8987 (tm-30) REVERT: t 26 LEU cc_start: 0.9045 (mp) cc_final: 0.8693 (tp) outliers start: 6 outliers final: 2 residues processed: 520 average time/residue: 0.1005 time to fit residues: 70.7852 Evaluate side-chains 303 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 GLN ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN k 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.038220 restraints weight = 57655.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039545 restraints weight = 30731.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.040477 restraints weight = 19433.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041137 restraints weight = 13488.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.041629 restraints weight = 9986.544| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9180 Z= 0.140 Angle : 0.649 5.482 12320 Z= 0.368 Chirality : 0.039 0.136 1460 Planarity : 0.002 0.019 1600 Dihedral : 5.537 37.720 1280 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % 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: -1.97 (0.23), residues: 1080 helix: -1.07 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG n 10 TYR 0.008 0.001 TYR c 8 HIS 0.001 0.000 HIS q 22 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9180) covalent geometry : angle 0.64856 (12320) hydrogen bonds : bond 0.03913 ( 481) hydrogen bonds : angle 5.34813 ( 1443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. 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: 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: B 15 ASP cc_start: 0.9565 (m-30) cc_final: 0.9360 (m-30) REVERT: B 17 LYS cc_start: 0.9485 (mptt) cc_final: 0.8956 (mmtt) REVERT: D 17 LYS cc_start: 0.9456 (mptt) cc_final: 0.9101 (mmtt) REVERT: A 20 GLU cc_start: 0.9147 (pp20) cc_final: 0.8924 (pp20) REVERT: E 1 GLN cc_start: 0.7587 (tp40) cc_final: 0.7297 (tp-100) REVERT: E 17 LYS cc_start: 0.9447 (mptt) cc_final: 0.9067 (mmtp) REVERT: F 20 GLU cc_start: 0.9134 (pp20) cc_final: 0.8924 (pp20) REVERT: H 1 GLN cc_start: 0.7201 (tp40) cc_final: 0.6707 (tp-100) REVERT: H 20 GLU cc_start: 0.9138 (pp20) cc_final: 0.8905 (pp20) REVERT: L 1 GLN cc_start: 0.7165 (tp40) cc_final: 0.6818 (tp-100) REVERT: L 13 GLU cc_start: 0.9198 (mp0) cc_final: 0.8925 (mp0) REVERT: L 17 LYS cc_start: 0.9406 (mptt) cc_final: 0.8853 (mmtp) REVERT: M 13 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8819 (tm-30) REVERT: M 17 LYS cc_start: 0.9523 (mptt) cc_final: 0.9038 (mmmm) REVERT: O 17 LYS cc_start: 0.9516 (mptt) cc_final: 0.9256 (mmtt) REVERT: P 17 LYS cc_start: 0.9389 (mptt) cc_final: 0.8871 (mmtt) REVERT: P 20 GLU cc_start: 0.8995 (pp20) cc_final: 0.8702 (pp20) REVERT: Q 18 ILE cc_start: 0.9220 (mt) cc_final: 0.9020 (mt) REVERT: a 1 GLN cc_start: 0.8423 (tp40) cc_final: 0.8217 (tp40) REVERT: a 17 LYS cc_start: 0.9468 (mptt) cc_final: 0.9124 (mmtp) REVERT: d 13 GLU cc_start: 0.9093 (mp0) cc_final: 0.8871 (mp0) REVERT: d 17 LYS cc_start: 0.9494 (mptt) cc_final: 0.9245 (mmtt) REVERT: e 1 GLN cc_start: 0.8737 (tp40) cc_final: 0.8520 (tp40) REVERT: f 29 GLN cc_start: 0.8706 (mt0) cc_final: 0.8494 (mt0) REVERT: g 13 GLU cc_start: 0.9097 (mp0) cc_final: 0.8805 (mp0) REVERT: g 17 LYS cc_start: 0.9461 (mptt) cc_final: 0.9048 (mmtp) REVERT: h 5 LEU cc_start: 0.9610 (mt) cc_final: 0.9343 (mt) REVERT: h 17 LYS cc_start: 0.9395 (mptt) cc_final: 0.9027 (mmtt) REVERT: i 1 GLN cc_start: 0.7294 (tp-100) cc_final: 0.7043 (tp40) REVERT: i 13 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8734 (tm-30) REVERT: i 17 LYS cc_start: 0.9509 (mptt) cc_final: 0.9056 (mmmm) REVERT: k 13 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8811 (tm-30) REVERT: k 17 LYS cc_start: 0.9512 (mptt) cc_final: 0.9073 (mmmm) REVERT: l 1 GLN cc_start: 0.7182 (tp40) cc_final: 0.6803 (tp40) REVERT: n 17 LYS cc_start: 0.9417 (mptt) cc_final: 0.8963 (mmtm) REVERT: o 17 LYS cc_start: 0.9497 (mptt) cc_final: 0.9073 (mmmm) REVERT: p 1 GLN cc_start: 0.8587 (tp40) cc_final: 0.8260 (tp-100) REVERT: p 12 LEU cc_start: 0.9608 (mm) cc_final: 0.9250 (tp) REVERT: q 1 GLN cc_start: 0.8296 (tp40) cc_final: 0.8038 (tp40) REVERT: r 4 ILE cc_start: 0.9507 (mt) cc_final: 0.9140 (mt) REVERT: r 17 LYS cc_start: 0.9490 (mptt) cc_final: 0.9100 (mmtt) REVERT: r 20 GLU cc_start: 0.9074 (pp20) cc_final: 0.8773 (pp20) REVERT: r 24 GLU cc_start: 0.9278 (tp30) cc_final: 0.9021 (tm-30) REVERT: r 26 LEU cc_start: 0.9006 (mp) cc_final: 0.8664 (tp) REVERT: t 1 GLN cc_start: 0.8543 (mt0) cc_final: 0.8307 (tp-100) REVERT: t 3 GLU cc_start: 0.9259 (pm20) cc_final: 0.9058 (pm20) REVERT: t 15 ASP cc_start: 0.9433 (m-30) cc_final: 0.9212 (m-30) REVERT: t 17 LYS cc_start: 0.9487 (mptt) cc_final: 0.9108 (mmtt) REVERT: t 18 ILE cc_start: 0.9176 (mt) cc_final: 0.8910 (mt) REVERT: t 20 GLU cc_start: 0.9009 (pp20) cc_final: 0.8705 (pp20) REVERT: t 24 GLU cc_start: 0.9291 (tp30) cc_final: 0.9007 (tm-30) REVERT: t 26 LEU cc_start: 0.9012 (mp) cc_final: 0.8675 (tp) outliers start: 1 outliers final: 0 residues processed: 529 average time/residue: 0.0996 time to fit residues: 71.2996 Evaluate side-chains 318 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036647 restraints weight = 58315.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037984 restraints weight = 29200.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.038848 restraints weight = 17529.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.039458 restraints weight = 11866.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.039879 restraints weight = 8654.676| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9180 Z= 0.227 Angle : 0.737 5.827 12320 Z= 0.423 Chirality : 0.044 0.186 1460 Planarity : 0.004 0.029 1600 Dihedral : 5.875 36.390 1280 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -2.03 (0.22), residues: 1080 helix: -1.11 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 10 TYR 0.010 0.001 TYR m 8 HIS 0.003 0.001 HIS r 22 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9180) covalent geometry : angle 0.73680 (12320) hydrogen bonds : bond 0.04412 ( 481) hydrogen bonds : angle 6.12410 ( 1443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. 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: 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: B 17 LYS cc_start: 0.9498 (mptt) cc_final: 0.8875 (mmtt) REVERT: C 17 LYS cc_start: 0.9489 (mptt) cc_final: 0.9107 (mmtm) REVERT: D 17 LYS cc_start: 0.9512 (mptt) cc_final: 0.9045 (mmtt) REVERT: A 1 GLN cc_start: 0.8284 (tp40) cc_final: 0.7978 (tp40) REVERT: E 1 GLN cc_start: 0.7650 (tp40) cc_final: 0.7376 (tp-100) REVERT: E 17 LYS cc_start: 0.9399 (mptt) cc_final: 0.8980 (mmtp) REVERT: E 29 GLN cc_start: 0.8709 (tt0) cc_final: 0.8496 (tt0) REVERT: F 20 GLU cc_start: 0.9149 (pp20) cc_final: 0.8914 (pp20) REVERT: H 1 GLN cc_start: 0.7283 (tp40) cc_final: 0.7050 (tp40) REVERT: H 20 GLU cc_start: 0.9171 (pp20) cc_final: 0.8968 (pp20) REVERT: L 1 GLN cc_start: 0.7146 (tp40) cc_final: 0.6798 (tp-100) REVERT: L 17 LYS cc_start: 0.9429 (mptt) cc_final: 0.8919 (mmtp) REVERT: P 12 LEU cc_start: 0.9436 (mm) cc_final: 0.9219 (tt) REVERT: P 17 LYS cc_start: 0.9512 (mptt) cc_final: 0.8977 (mmtt) REVERT: P 20 GLU cc_start: 0.9105 (pp20) cc_final: 0.8788 (pp20) REVERT: Q 1 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7555 (tm-30) REVERT: R 17 LYS cc_start: 0.9641 (mmtt) cc_final: 0.9256 (mmtm) REVERT: R 20 GLU cc_start: 0.9080 (pm20) cc_final: 0.8853 (pm20) REVERT: S 17 LYS cc_start: 0.9578 (mptt) cc_final: 0.9203 (mmtp) REVERT: a 13 GLU cc_start: 0.9157 (pm20) cc_final: 0.8833 (mp0) REVERT: a 17 LYS cc_start: 0.9529 (mptt) cc_final: 0.9025 (mmtt) REVERT: b 13 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9160 (mp0) REVERT: b 20 GLU cc_start: 0.9116 (pp20) cc_final: 0.8898 (pp20) REVERT: c 13 GLU cc_start: 0.9137 (pm20) cc_final: 0.8904 (pm20) REVERT: c 17 LYS cc_start: 0.9474 (mptt) cc_final: 0.8976 (mmtp) REVERT: e 1 GLN cc_start: 0.8889 (tp40) cc_final: 0.8533 (tp40) REVERT: e 27 LYS cc_start: 0.9233 (tmtt) cc_final: 0.8985 (ttmt) REVERT: f 29 GLN cc_start: 0.8529 (mt0) cc_final: 0.8273 (mt0) REVERT: g 13 GLU cc_start: 0.9103 (mp0) cc_final: 0.8888 (mp0) REVERT: g 17 LYS cc_start: 0.9460 (mptt) cc_final: 0.8965 (mmtp) REVERT: g 27 LYS cc_start: 0.9288 (tmtt) cc_final: 0.9051 (ttmt) REVERT: h 12 LEU cc_start: 0.9492 (mm) cc_final: 0.9173 (tp) REVERT: h 17 LYS cc_start: 0.9489 (mptt) cc_final: 0.9113 (mmtp) REVERT: h 20 GLU cc_start: 0.9169 (pp20) cc_final: 0.8895 (pp20) REVERT: l 1 GLN cc_start: 0.7183 (tp40) cc_final: 0.6822 (tp-100) REVERT: l 15 ASP cc_start: 0.9414 (m-30) cc_final: 0.9172 (m-30) REVERT: l 17 LYS cc_start: 0.9418 (mptt) cc_final: 0.8995 (mmtp) REVERT: l 18 ILE cc_start: 0.9242 (mp) cc_final: 0.9003 (mp) REVERT: m 11 ILE cc_start: 0.9409 (mt) cc_final: 0.9074 (mt) REVERT: m 12 LEU cc_start: 0.9556 (mm) cc_final: 0.9311 (mm) REVERT: n 12 LEU cc_start: 0.9615 (mm) cc_final: 0.9331 (tp) REVERT: n 17 LYS cc_start: 0.9470 (mptt) cc_final: 0.9007 (mmtm) REVERT: n 20 GLU cc_start: 0.9069 (pp20) cc_final: 0.8787 (pp20) REVERT: o 17 LYS cc_start: 0.9480 (mptt) cc_final: 0.9111 (mmmm) REVERT: p 1 GLN cc_start: 0.8759 (tp40) cc_final: 0.8550 (tp-100) REVERT: p 12 LEU cc_start: 0.9612 (mm) cc_final: 0.9314 (tp) REVERT: p 17 LYS cc_start: 0.9467 (mptt) cc_final: 0.9011 (mmtm) REVERT: p 20 GLU cc_start: 0.9108 (pp20) cc_final: 0.8829 (pp20) REVERT: r 15 ASP cc_start: 0.9459 (m-30) cc_final: 0.9240 (m-30) REVERT: r 17 LYS cc_start: 0.9489 (mptt) cc_final: 0.9087 (mmtt) REVERT: r 18 ILE cc_start: 0.9249 (mt) cc_final: 0.8976 (mt) REVERT: r 20 GLU cc_start: 0.9131 (pp20) cc_final: 0.8784 (pp20) REVERT: r 24 GLU cc_start: 0.9338 (tp30) cc_final: 0.9033 (tm-30) REVERT: r 26 LEU cc_start: 0.9082 (mp) cc_final: 0.8745 (tp) REVERT: s 17 LYS cc_start: 0.9516 (mptt) cc_final: 0.9134 (mmtp) REVERT: t 1 GLN cc_start: 0.8523 (mt0) cc_final: 0.8267 (tp-100) REVERT: t 15 ASP cc_start: 0.9454 (m-30) cc_final: 0.9218 (m-30) REVERT: t 17 LYS cc_start: 0.9487 (mptt) cc_final: 0.9116 (mmtt) REVERT: t 18 ILE cc_start: 0.9250 (mt) cc_final: 0.8997 (mt) REVERT: t 20 GLU cc_start: 0.9138 (pp20) cc_final: 0.8838 (pp20) REVERT: t 24 GLU cc_start: 0.9340 (tp30) cc_final: 0.9032 (tm-30) REVERT: t 26 LEU cc_start: 0.9058 (mp) cc_final: 0.8722 (tp) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1021 time to fit residues: 71.2133 Evaluate side-chains 323 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.045321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040434 restraints weight = 57914.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041799 restraints weight = 29346.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042681 restraints weight = 17528.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043296 restraints weight = 11581.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043727 restraints weight = 8135.570| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.188 Angle : 0.768 5.772 12320 Z= 0.441 Chirality : 0.043 0.161 1460 Planarity : 0.003 0.024 1600 Dihedral : 5.839 37.087 1280 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -1.77 (0.22), residues: 1080 helix: -0.94 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 10 TYR 0.006 0.001 TYR P 8 HIS 0.002 0.000 HIS r 22 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9180) covalent geometry : angle 0.76757 (12320) hydrogen bonds : bond 0.04656 ( 481) hydrogen bonds : angle 6.09284 ( 1443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN R 1 " (corrupted residue). Skipping it. 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9481 (mptt) cc_final: 0.8874 (mmtt) REVERT: D 17 LYS cc_start: 0.9537 (mptt) cc_final: 0.9122 (mmtt) REVERT: A 17 LYS cc_start: 0.9523 (mptt) cc_final: 0.9038 (mmtm) REVERT: E 1 GLN cc_start: 0.7671 (tp40) cc_final: 0.7407 (tp-100) REVERT: E 17 LYS cc_start: 0.9406 (mptt) cc_final: 0.9140 (mmtp) REVERT: H 1 GLN cc_start: 0.7323 (tp40) cc_final: 0.6893 (tp-100) REVERT: L 1 GLN cc_start: 0.7150 (tp40) cc_final: 0.6741 (tp-100) REVERT: O 12 LEU cc_start: 0.9440 (mm) cc_final: 0.9186 (tp) REVERT: O 17 LYS cc_start: 0.9578 (mptt) cc_final: 0.9231 (mmtt) REVERT: P 17 LYS cc_start: 0.9396 (mptt) cc_final: 0.8910 (mmtm) REVERT: P 20 GLU cc_start: 0.8939 (pp20) cc_final: 0.8665 (pp20) REVERT: Q 1 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7642 (tm-30) REVERT: R 17 LYS cc_start: 0.9621 (mmtt) cc_final: 0.9304 (mmtm) REVERT: S 12 LEU cc_start: 0.9553 (mm) cc_final: 0.9326 (tp) REVERT: a 13 GLU cc_start: 0.9090 (pm20) cc_final: 0.8872 (mp0) REVERT: a 17 LYS cc_start: 0.9573 (mptt) cc_final: 0.9223 (mmtp) REVERT: c 18 ILE cc_start: 0.9279 (mt) cc_final: 0.9061 (mt) REVERT: d 13 GLU cc_start: 0.9076 (mp0) cc_final: 0.8740 (mp0) REVERT: d 17 LYS cc_start: 0.9472 (mptt) cc_final: 0.9049 (mmtp) REVERT: d 20 GLU cc_start: 0.8908 (pm20) cc_final: 0.8681 (pm20) REVERT: e 17 LYS cc_start: 0.9513 (mptt) cc_final: 0.9220 (mmtm) REVERT: e 27 LYS cc_start: 0.9175 (tmtt) cc_final: 0.8971 (tptp) REVERT: f 20 GLU cc_start: 0.9074 (pm20) cc_final: 0.8842 (pm20) REVERT: g 13 GLU cc_start: 0.9090 (mp0) cc_final: 0.8634 (mp0) REVERT: g 17 LYS cc_start: 0.9428 (mptt) cc_final: 0.9130 (mmtt) REVERT: g 27 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8971 (ttmt) REVERT: h 12 LEU cc_start: 0.9431 (mm) cc_final: 0.9173 (tp) REVERT: h 17 LYS cc_start: 0.9428 (mptt) cc_final: 0.9054 (mmtp) REVERT: h 20 GLU cc_start: 0.8981 (pp20) cc_final: 0.8739 (pp20) REVERT: j 17 LYS cc_start: 0.9470 (mptt) cc_final: 0.8989 (mmtp) REVERT: l 17 LYS cc_start: 0.9459 (mptt) cc_final: 0.8992 (mmtp) REVERT: n 12 LEU cc_start: 0.9544 (mm) cc_final: 0.9277 (tp) REVERT: n 17 LYS cc_start: 0.9384 (mptt) cc_final: 0.8917 (mmtm) REVERT: n 20 GLU cc_start: 0.8907 (pp20) cc_final: 0.8703 (pp20) REVERT: o 17 LYS cc_start: 0.9448 (mptt) cc_final: 0.9028 (mmmm) REVERT: p 12 LEU cc_start: 0.9531 (mm) cc_final: 0.9214 (tp) REVERT: p 17 LYS cc_start: 0.9414 (mptt) cc_final: 0.8916 (mmtm) REVERT: q 1 GLN cc_start: 0.8700 (tp40) cc_final: 0.8418 (tp40) REVERT: q 3 GLU cc_start: 0.9185 (pm20) cc_final: 0.8855 (pm20) REVERT: r 15 ASP cc_start: 0.9364 (m-30) cc_final: 0.9163 (m-30) REVERT: r 17 LYS cc_start: 0.9427 (mptt) cc_final: 0.9026 (mmtt) REVERT: r 18 ILE cc_start: 0.9244 (mt) cc_final: 0.9021 (mt) REVERT: r 20 GLU cc_start: 0.8964 (pp20) cc_final: 0.8736 (pp20) REVERT: r 26 LEU cc_start: 0.9006 (mp) cc_final: 0.8654 (tp) REVERT: s 17 LYS cc_start: 0.9437 (mptt) cc_final: 0.9115 (mmtp) REVERT: t 1 GLN cc_start: 0.8508 (mt0) cc_final: 0.8234 (tp-100) REVERT: t 15 ASP cc_start: 0.9350 (m-30) cc_final: 0.9130 (m-30) REVERT: t 17 LYS cc_start: 0.9428 (mptt) cc_final: 0.9063 (mmtt) REVERT: t 18 ILE cc_start: 0.9240 (mt) cc_final: 0.9029 (mt) REVERT: t 20 GLU cc_start: 0.8906 (pp20) cc_final: 0.8698 (pp20) REVERT: t 24 GLU cc_start: 0.9100 (tp30) cc_final: 0.8889 (tm-30) REVERT: t 26 LEU cc_start: 0.8981 (mp) cc_final: 0.8659 (tp) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.0966 time to fit residues: 68.6040 Evaluate side-chains 324 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.037694 restraints weight = 57595.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039020 restraints weight = 29046.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039895 restraints weight = 17471.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.040493 restraints weight = 11781.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.040925 restraints weight = 8575.525| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.201 Angle : 0.818 6.493 12320 Z= 0.472 Chirality : 0.045 0.188 1460 Planarity : 0.003 0.026 1600 Dihedral : 5.835 38.803 1280 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.69 (0.22), residues: 1080 helix: -0.90 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG n 10 TYR 0.007 0.001 TYR a 8 HIS 0.002 0.001 HIS r 22 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9180) covalent geometry : angle 0.81836 (12320) hydrogen bonds : bond 0.04869 ( 481) hydrogen bonds : angle 6.25052 ( 1443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN R 1 " (corrupted residue). Skipping it. 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: 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: B 17 LYS cc_start: 0.9531 (mptt) cc_final: 0.8976 (mmtt) REVERT: D 17 LYS cc_start: 0.9556 (mptt) cc_final: 0.9198 (mmtp) REVERT: A 17 LYS cc_start: 0.9551 (mptt) cc_final: 0.9093 (mmtm) REVERT: E 1 GLN cc_start: 0.7668 (tp40) cc_final: 0.7375 (tp-100) REVERT: E 17 LYS cc_start: 0.9448 (mptt) cc_final: 0.9164 (mmtp) REVERT: H 1 GLN cc_start: 0.7375 (tp40) cc_final: 0.7041 (tp40) REVERT: H 20 GLU cc_start: 0.9075 (pp20) cc_final: 0.8864 (pp20) REVERT: J 13 GLU cc_start: 0.9083 (pm20) cc_final: 0.8756 (mp0) REVERT: J 17 LYS cc_start: 0.9377 (mptt) cc_final: 0.8835 (mmtp) REVERT: L 1 GLN cc_start: 0.7133 (tp40) cc_final: 0.6589 (tp-100) REVERT: L 5 LEU cc_start: 0.9715 (mt) cc_final: 0.9467 (mt) REVERT: O 12 LEU cc_start: 0.9465 (mm) cc_final: 0.9204 (tp) REVERT: O 17 LYS cc_start: 0.9586 (mptt) cc_final: 0.9209 (mmtt) REVERT: P 12 LEU cc_start: 0.9503 (mm) cc_final: 0.9096 (tp) REVERT: P 17 LYS cc_start: 0.9414 (mptt) cc_final: 0.8894 (mmtm) REVERT: P 20 GLU cc_start: 0.9052 (pp20) cc_final: 0.8751 (pp20) REVERT: Q 1 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7430 (tm-30) REVERT: R 17 LYS cc_start: 0.9648 (mmtt) cc_final: 0.9314 (mmtm) REVERT: S 12 LEU cc_start: 0.9581 (mm) cc_final: 0.9325 (tp) REVERT: T 1 GLN cc_start: 0.8513 (tp40) cc_final: 0.8201 (tp40) REVERT: b 13 GLU cc_start: 0.9031 (mp0) cc_final: 0.8695 (mp0) REVERT: b 17 LYS cc_start: 0.9404 (mptt) cc_final: 0.9073 (mmtt) REVERT: c 18 ILE cc_start: 0.9293 (mt) cc_final: 0.9066 (mt) REVERT: e 3 GLU cc_start: 0.8904 (pm20) cc_final: 0.8676 (pm20) REVERT: e 17 LYS cc_start: 0.9546 (mptt) cc_final: 0.9280 (mmtm) REVERT: f 17 LYS cc_start: 0.9589 (mptt) cc_final: 0.9225 (mmtt) REVERT: g 13 GLU cc_start: 0.9208 (mp0) cc_final: 0.8754 (mp0) REVERT: g 17 LYS cc_start: 0.9598 (mptt) cc_final: 0.9163 (mmtp) REVERT: g 27 LYS cc_start: 0.9240 (tmtt) cc_final: 0.8984 (ttmt) REVERT: h 12 LEU cc_start: 0.9475 (mm) cc_final: 0.9211 (tp) REVERT: h 17 LYS cc_start: 0.9429 (mptt) cc_final: 0.9059 (mmtp) REVERT: h 20 GLU cc_start: 0.9049 (pp20) cc_final: 0.8778 (pp20) REVERT: l 15 ASP cc_start: 0.9433 (m-30) cc_final: 0.9191 (m-30) REVERT: n 12 LEU cc_start: 0.9578 (mm) cc_final: 0.9284 (tp) REVERT: n 17 LYS cc_start: 0.9464 (mptt) cc_final: 0.9039 (mmtm) REVERT: n 20 GLU cc_start: 0.9018 (pp20) cc_final: 0.8755 (pp20) REVERT: o 17 LYS cc_start: 0.9486 (mptt) cc_final: 0.9081 (mmmm) REVERT: p 12 LEU cc_start: 0.9571 (mm) cc_final: 0.9160 (tp) REVERT: p 17 LYS cc_start: 0.9452 (mptt) cc_final: 0.8984 (mmtm) REVERT: p 20 GLU cc_start: 0.8969 (pp20) cc_final: 0.8755 (pp20) REVERT: q 1 GLN cc_start: 0.8658 (tp40) cc_final: 0.8297 (tp40) REVERT: q 3 GLU cc_start: 0.9273 (pm20) cc_final: 0.8958 (pm20) REVERT: r 15 ASP cc_start: 0.9427 (m-30) cc_final: 0.9196 (m-30) REVERT: r 17 LYS cc_start: 0.9449 (mptt) cc_final: 0.9062 (mmtt) REVERT: r 18 ILE cc_start: 0.9226 (mt) cc_final: 0.8973 (mt) REVERT: r 20 GLU cc_start: 0.9080 (pp20) cc_final: 0.8744 (pp20) REVERT: r 26 LEU cc_start: 0.9011 (mp) cc_final: 0.8688 (tp) REVERT: s 17 LYS cc_start: 0.9532 (mptt) cc_final: 0.9289 (mmtp) REVERT: t 1 GLN cc_start: 0.8595 (mt0) cc_final: 0.8273 (tp-100) REVERT: t 15 ASP cc_start: 0.9430 (m-30) cc_final: 0.9209 (m-30) REVERT: t 17 LYS cc_start: 0.9456 (mptt) cc_final: 0.9090 (mmtt) REVERT: t 18 ILE cc_start: 0.9224 (mt) cc_final: 0.9006 (mt) REVERT: t 20 GLU cc_start: 0.9023 (pp20) cc_final: 0.8751 (pp20) REVERT: t 24 GLU cc_start: 0.9225 (tp30) cc_final: 0.8994 (tm-30) REVERT: t 26 LEU cc_start: 0.9016 (mp) cc_final: 0.8691 (tp) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.0950 time to fit residues: 66.7205 Evaluate side-chains 320 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.043103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037807 restraints weight = 58434.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039142 restraints weight = 30011.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040054 restraints weight = 18286.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.040680 restraints weight = 12284.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.041108 restraints weight = 8890.084| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.200 Angle : 0.856 6.781 12320 Z= 0.494 Chirality : 0.045 0.177 1460 Planarity : 0.003 0.024 1600 Dihedral : 5.770 40.937 1280 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.54 (0.23), residues: 1080 helix: -0.81 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG n 10 TYR 0.011 0.001 TYR m 8 HIS 0.002 0.000 HIS r 22 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9180) covalent geometry : angle 0.85643 (12320) hydrogen bonds : bond 0.05046 ( 481) hydrogen bonds : angle 6.25161 ( 1443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. 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: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN R 1 " (corrupted residue). Skipping it. 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: 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: B 15 ASP cc_start: 0.9611 (m-30) cc_final: 0.9376 (m-30) REVERT: B 17 LYS cc_start: 0.9490 (mptt) cc_final: 0.8932 (mmtt) REVERT: D 17 LYS cc_start: 0.9556 (mptt) cc_final: 0.9165 (mmtt) REVERT: A 17 LYS cc_start: 0.9550 (mptt) cc_final: 0.9080 (mmtm) REVERT: A 20 GLU cc_start: 0.9039 (pp20) cc_final: 0.8828 (pp20) REVERT: E 17 LYS cc_start: 0.9441 (mptt) cc_final: 0.9159 (mmtp) REVERT: H 1 GLN cc_start: 0.7349 (tp40) cc_final: 0.6909 (tp40) REVERT: H 20 GLU cc_start: 0.9098 (pp20) cc_final: 0.8864 (pp20) REVERT: J 13 GLU cc_start: 0.9099 (pm20) cc_final: 0.8793 (mp0) REVERT: J 17 LYS cc_start: 0.9405 (mptt) cc_final: 0.8829 (mmtp) REVERT: L 1 GLN cc_start: 0.7063 (tp40) cc_final: 0.6634 (tp-100) REVERT: O 12 LEU cc_start: 0.9451 (mm) cc_final: 0.9209 (tp) REVERT: P 17 LYS cc_start: 0.9399 (mptt) cc_final: 0.8912 (mmtm) REVERT: P 20 GLU cc_start: 0.9035 (pp20) cc_final: 0.8743 (pp20) REVERT: Q 1 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7731 (tm-30) REVERT: Q 13 GLU cc_start: 0.9172 (pm20) cc_final: 0.8880 (pm20) REVERT: Q 17 LYS cc_start: 0.9438 (mptt) cc_final: 0.9075 (mmtp) REVERT: Q 18 ILE cc_start: 0.9288 (mt) cc_final: 0.9079 (mt) REVERT: R 17 LYS cc_start: 0.9643 (mmtt) cc_final: 0.9297 (mmtm) REVERT: S 12 LEU cc_start: 0.9570 (mm) cc_final: 0.9315 (tp) REVERT: S 27 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8818 (ttmm) REVERT: T 1 GLN cc_start: 0.8640 (tp40) cc_final: 0.8318 (tp40) REVERT: b 13 GLU cc_start: 0.9099 (mp0) cc_final: 0.8783 (mp0) REVERT: b 17 LYS cc_start: 0.9432 (mptt) cc_final: 0.9084 (mmtt) REVERT: c 18 ILE cc_start: 0.9255 (mt) cc_final: 0.9031 (mt) REVERT: e 3 GLU cc_start: 0.8960 (pm20) cc_final: 0.8711 (pm20) REVERT: e 27 LYS cc_start: 0.9179 (tmtt) cc_final: 0.8919 (ttmm) REVERT: f 17 LYS cc_start: 0.9583 (mptt) cc_final: 0.9243 (mmtp) REVERT: g 27 LYS cc_start: 0.9230 (tmtt) cc_final: 0.8987 (ttmt) REVERT: h 20 GLU cc_start: 0.9052 (pp20) cc_final: 0.8776 (pp20) REVERT: n 12 LEU cc_start: 0.9561 (mm) cc_final: 0.9200 (tp) REVERT: n 17 LYS cc_start: 0.9460 (mptt) cc_final: 0.9009 (mmtm) REVERT: n 20 GLU cc_start: 0.8992 (pp20) cc_final: 0.8727 (pp20) REVERT: o 17 LYS cc_start: 0.9486 (mptt) cc_final: 0.9067 (mmmm) REVERT: p 1 GLN cc_start: 0.8639 (tp40) cc_final: 0.8330 (tm-30) REVERT: p 17 LYS cc_start: 0.9430 (mptt) cc_final: 0.8951 (mmtm) REVERT: p 20 GLU cc_start: 0.8991 (pp20) cc_final: 0.8779 (pp20) REVERT: q 1 GLN cc_start: 0.8718 (tp40) cc_final: 0.8376 (tp40) REVERT: q 3 GLU cc_start: 0.9337 (pm20) cc_final: 0.9013 (pm20) REVERT: r 15 ASP cc_start: 0.9432 (m-30) cc_final: 0.9145 (m-30) REVERT: r 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.9135 (mmtt) REVERT: r 20 GLU cc_start: 0.9048 (pp20) cc_final: 0.8712 (pp20) REVERT: r 26 LEU cc_start: 0.8994 (mp) cc_final: 0.8704 (tp) REVERT: t 1 GLN cc_start: 0.8605 (mt0) cc_final: 0.8271 (tp-100) REVERT: t 17 LYS cc_start: 0.9469 (mptt) cc_final: 0.9103 (mmtt) REVERT: t 20 GLU cc_start: 0.9008 (pp20) cc_final: 0.8761 (pp20) REVERT: t 24 GLU cc_start: 0.9232 (tp30) cc_final: 0.9013 (tm-30) REVERT: t 26 LEU cc_start: 0.9024 (mp) cc_final: 0.8730 (tp) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.0985 time to fit residues: 69.8131 Evaluate side-chains 331 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 69 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 0.0270 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 1 GLN ** i 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038294 restraints weight = 56106.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039647 restraints weight = 28707.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.040553 restraints weight = 17551.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041186 restraints weight = 11910.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.041641 restraints weight = 8678.375| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.197 Angle : 0.867 6.912 12320 Z= 0.497 Chirality : 0.044 0.187 1460 Planarity : 0.003 0.020 1600 Dihedral : 5.709 40.469 1280 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.46 (0.23), residues: 1080 helix: -0.76 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG q 6 TYR 0.008 0.001 TYR a 8 HIS 0.002 0.000 HIS r 22 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9180) covalent geometry : angle 0.86745 (12320) hydrogen bonds : bond 0.05036 ( 481) hydrogen bonds : angle 6.14492 ( 1443) =============================================================================== Job complete usr+sys time: 1695.60 seconds wall clock time: 29 minutes 48.63 seconds (1788.63 seconds total)