Starting phenix.real_space_refine on Thu Mar 13 09:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wky_21813/03_2025/6wky_21813.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wky_21813/03_2025/6wky_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2025/6wky_21813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2025/6wky_21813.map" model { file = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2025/6wky_21813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wky_21813/03_2025/6wky_21813.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.88, per 1000 atoms: 0.64 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: 2.30 Conformation dependent library (CDL) restraints added in 989.6 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: 0.57 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: 2.15 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.990 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- 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= 0.404 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.005 0.002 HIS F 22 TYR 0.005 0.001 TYR T 8 ARG 0.003 0.001 ARG O 10 *********************** 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 : 1.103 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: 0.9229 (tptp) REVERT: M 3 GLU cc_start: 0.8902 (tt0) cc_final: 0.8698 (tp30) REVERT: M 13 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8762 (mt-10) REVERT: P 3 GLU cc_start: 0.8964 (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: 0.8230 (tp-100) REVERT: Q 3 GLU cc_start: 0.9221 (tt0) cc_final: 0.8880 (tp30) REVERT: Q 5 LEU cc_start: 0.9416 (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: 0.9092 (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: 0.9582 (mptt) cc_final: 0.9330 (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: 0.8842 (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: 0.2293 time to fit residues: 184.9034 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 : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.0030 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 overall best weight: 1.6194 ------------------------------------------------------------------------------- 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 = 0.3093 r_free = 0.3093 target = 0.042088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036867 restraints weight = 55786.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.038130 restraints weight = 28715.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038993 restraints weight = 17683.531| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9180 Z= 0.185 Angle : 0.611 4.710 12320 Z= 0.347 Chirality : 0.038 0.128 1460 Planarity : 0.004 0.026 1600 Dihedral : 5.580 31.773 1280 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.41 % Allowed : 5.49 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.18), residues: 1080 helix: -3.13 (0.11), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS j 22 TYR 0.006 0.001 TYR a 8 ARG 0.004 0.001 ARG e 10 *********************** 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 614 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 586 time to evaluate : 1.043 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: B 1 GLN cc_start: 0.7302 (tp40) cc_final: 0.6955 (tp40) REVERT: B 3 GLU cc_start: 0.8937 (tt0) cc_final: 0.8702 (tp30) REVERT: B 13 GLU cc_start: 0.9161 (tt0) cc_final: 0.8908 (mt-10) REVERT: A 17 LYS cc_start: 0.9570 (mptt) cc_final: 0.9092 (mmtm) REVERT: E 1 GLN cc_start: 0.7089 (tp40) cc_final: 0.6541 (tp-100) REVERT: F 13 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8538 (mp0) REVERT: F 17 LYS cc_start: 0.9474 (mptt) cc_final: 0.9124 (mmtt) REVERT: F 20 GLU cc_start: 0.9139 (pp20) cc_final: 0.8886 (pp20) REVERT: H 1 GLN cc_start: 0.7347 (tp40) cc_final: 0.7043 (tp40) REVERT: H 20 GLU cc_start: 0.9127 (pp20) cc_final: 0.8879 (pp20) REVERT: I 5 LEU cc_start: 0.9699 (mt) cc_final: 0.9413 (mt) REVERT: I 13 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8843 (mt-10) REVERT: K 13 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8998 (mp0) REVERT: L 1 GLN cc_start: 0.7148 (tp40) cc_final: 0.6747 (tp40) REVERT: L 5 LEU cc_start: 0.9700 (mt) cc_final: 0.9456 (mt) REVERT: L 13 GLU cc_start: 0.9019 (mp0) cc_final: 0.8663 (mp0) REVERT: L 17 LYS cc_start: 0.9435 (mptt) cc_final: 0.8922 (mmtt) REVERT: M 5 LEU cc_start: 0.9767 (mt) cc_final: 0.9236 (mp) REVERT: O 17 LYS cc_start: 0.9562 (mptt) cc_final: 0.9061 (mmtm) REVERT: P 17 LYS cc_start: 0.9613 (mptt) cc_final: 0.9107 (mmtm) REVERT: Q 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.9029 (mmtt) REVERT: T 1 GLN cc_start: 0.7240 (tp40) cc_final: 0.6940 (tp40) REVERT: T 5 LEU cc_start: 0.9684 (mt) cc_final: 0.9438 (mt) REVERT: e 3 GLU cc_start: 0.9117 (tt0) cc_final: 0.8743 (tp30) REVERT: e 17 LYS cc_start: 0.9406 (mptt) cc_final: 0.8968 (mmtt) REVERT: e 27 LYS cc_start: 0.9364 (tptm) cc_final: 0.9031 (mmmt) REVERT: f 3 GLU cc_start: 0.8958 (tt0) cc_final: 0.8751 (tp30) REVERT: f 11 ILE cc_start: 0.9325 (mt) cc_final: 0.9071 (mt) REVERT: g 13 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8762 (mp0) REVERT: g 17 LYS cc_start: 0.9438 (mptt) cc_final: 0.8972 (mmtt) REVERT: h 5 LEU cc_start: 0.9485 (mt) cc_final: 0.9198 (mt) REVERT: i 1 GLN cc_start: 0.6957 (tp40) cc_final: 0.6573 (tp-100) REVERT: i 13 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8809 (tm-30) REVERT: i 17 LYS cc_start: 0.9464 (mptt) cc_final: 0.9151 (mmmm) REVERT: k 13 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8791 (tm-30) REVERT: l 1 GLN cc_start: 0.6758 (tp40) cc_final: 0.6472 (tp40) REVERT: l 5 LEU cc_start: 0.9753 (mt) cc_final: 0.9507 (mt) REVERT: m 3 GLU cc_start: 0.9007 (tt0) cc_final: 0.8766 (tp30) REVERT: n 3 GLU cc_start: 0.9010 (tt0) cc_final: 0.8778 (tp30) REVERT: o 13 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8707 (mt-10) REVERT: p 1 GLN cc_start: 0.7395 (tp40) cc_final: 0.7122 (tp40) REVERT: p 3 GLU cc_start: 0.8906 (tt0) cc_final: 0.8630 (tp30) REVERT: q 5 LEU cc_start: 0.9213 (mp) cc_final: 0.9011 (mp) REVERT: q 13 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8533 (mt-10) REVERT: r 3 GLU cc_start: 0.8826 (tt0) cc_final: 0.8577 (tp30) REVERT: r 17 LYS cc_start: 0.9547 (mptt) cc_final: 0.9128 (mmtt) REVERT: r 20 GLU cc_start: 0.9199 (pp20) cc_final: 0.8999 (pp20) REVERT: r 26 LEU cc_start: 0.9047 (mp) cc_final: 0.8499 (tp) REVERT: t 17 LYS cc_start: 0.9521 (mptt) cc_final: 0.9100 (mmtt) REVERT: t 24 GLU cc_start: 0.9260 (tp30) cc_final: 0.9043 (tp30) REVERT: t 26 LEU cc_start: 0.8987 (mp) cc_final: 0.8518 (tp) outliers start: 28 outliers final: 0 residues processed: 586 average time/residue: 0.2891 time to fit residues: 228.4533 Evaluate side-chains 315 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 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 = 0.3137 r_free = 0.3137 target = 0.043728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.038394 restraints weight = 57452.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039752 restraints weight = 28676.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.040665 restraints weight = 17324.147| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9180 Z= 0.183 Angle : 0.581 4.644 12320 Z= 0.335 Chirality : 0.039 0.136 1460 Planarity : 0.003 0.032 1600 Dihedral : 5.370 33.571 1280 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.07 % Allowed : 4.27 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.20), residues: 1080 helix: -2.35 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 22 TYR 0.007 0.001 TYR f 8 ARG 0.002 0.000 ARG e 10 *********************** 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 583 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 566 time to evaluate : 1.875 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 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: D 13 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9081 (mt-10) REVERT: A 1 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7175 (tp40) REVERT: E 1 GLN cc_start: 0.7314 (tp40) cc_final: 0.7079 (tp40) REVERT: F 20 GLU cc_start: 0.9154 (pp20) cc_final: 0.8921 (pp20) REVERT: H 1 GLN cc_start: 0.7284 (tp40) cc_final: 0.6885 (tp-100) REVERT: H 20 GLU cc_start: 0.9231 (pp20) cc_final: 0.9025 (pp20) REVERT: I 1 GLN cc_start: 0.7186 (tp-100) cc_final: 0.6984 (tp-100) REVERT: I 29 GLN cc_start: 0.8484 (tt0) cc_final: 0.8189 (tm-30) REVERT: L 1 GLN cc_start: 0.7224 (tp40) cc_final: 0.6913 (tp40) REVERT: M 13 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8849 (tm-30) REVERT: M 17 LYS cc_start: 0.9478 (mptt) cc_final: 0.9016 (mmmm) REVERT: Q 1 GLN cc_start: 0.7228 (tp40) cc_final: 0.6989 (tp-100) REVERT: Q 5 LEU cc_start: 0.9666 (mt) cc_final: 0.9314 (mt) REVERT: S 17 LYS cc_start: 0.9510 (mptt) cc_final: 0.9149 (mmtt) REVERT: T 5 LEU cc_start: 0.9622 (mt) cc_final: 0.9348 (mp) REVERT: T 20 GLU cc_start: 0.9087 (pp20) cc_final: 0.8881 (pp20) REVERT: a 3 GLU cc_start: 0.9090 (pm20) cc_final: 0.8815 (pm20) REVERT: a 17 LYS cc_start: 0.9500 (mptt) cc_final: 0.9097 (mmtp) REVERT: e 17 LYS cc_start: 0.9384 (mptt) cc_final: 0.9025 (mmtt) REVERT: f 3 GLU cc_start: 0.8983 (tt0) cc_final: 0.8731 (tp30) REVERT: f 17 LYS cc_start: 0.9623 (mptt) cc_final: 0.9209 (mmtp) REVERT: h 5 LEU cc_start: 0.9623 (mt) cc_final: 0.9270 (mt) REVERT: h 20 GLU cc_start: 0.9147 (pp20) cc_final: 0.8884 (pp20) REVERT: i 1 GLN cc_start: 0.7222 (tp40) cc_final: 0.6961 (tp40) REVERT: i 13 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8795 (tm-30) REVERT: i 17 LYS cc_start: 0.9480 (mptt) cc_final: 0.8741 (mmmm) REVERT: j 17 LYS cc_start: 0.9522 (mptt) cc_final: 0.9064 (mmtp) REVERT: k 13 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8785 (tm-30) REVERT: k 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.8698 (mmmm) REVERT: l 5 LEU cc_start: 0.9740 (mt) cc_final: 0.9488 (mt) REVERT: m 3 GLU cc_start: 0.9017 (tt0) cc_final: 0.8768 (tp30) REVERT: m 17 LYS cc_start: 0.9512 (mptt) cc_final: 0.9114 (mmtm) REVERT: n 3 GLU cc_start: 0.8892 (tt0) cc_final: 0.8689 (tp30) REVERT: n 20 GLU cc_start: 0.9138 (pp20) cc_final: 0.8874 (pp20) REVERT: o 11 ILE cc_start: 0.9394 (mt) cc_final: 0.9129 (mt) REVERT: p 20 GLU cc_start: 0.9107 (pp20) cc_final: 0.8875 (pp20) REVERT: q 1 GLN cc_start: 0.6946 (tp40) cc_final: 0.6450 (tp40) REVERT: q 3 GLU cc_start: 0.9179 (pm20) cc_final: 0.8920 (pm20) REVERT: q 5 LEU cc_start: 0.9358 (mp) cc_final: 0.9116 (mp) REVERT: q 18 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9128 (mp) REVERT: r 3 GLU cc_start: 0.8763 (tt0) cc_final: 0.8480 (tp30) REVERT: r 17 LYS cc_start: 0.9512 (mptt) cc_final: 0.9102 (mmtt) REVERT: r 20 GLU cc_start: 0.9163 (pp20) cc_final: 0.8954 (pp20) REVERT: r 24 GLU cc_start: 0.9273 (tp30) cc_final: 0.8930 (tm-30) REVERT: r 26 LEU cc_start: 0.9024 (mp) cc_final: 0.8585 (tp) REVERT: s 18 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9126 (mp) REVERT: t 17 LYS cc_start: 0.9498 (mptt) cc_final: 0.9118 (mmtt) REVERT: t 20 GLU cc_start: 0.9095 (pp20) cc_final: 0.8819 (pp20) REVERT: t 26 LEU cc_start: 0.9037 (mp) cc_final: 0.8597 (tp) outliers start: 17 outliers final: 0 residues processed: 566 average time/residue: 0.2298 time to fit residues: 173.9363 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 : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.037836 restraints weight = 57032.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039153 restraints weight = 28500.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040028 restraints weight = 17076.024| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9180 Z= 0.213 Angle : 0.626 4.698 12320 Z= 0.365 Chirality : 0.040 0.130 1460 Planarity : 0.003 0.038 1600 Dihedral : 5.500 36.076 1280 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.85 % Allowed : 3.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.22), residues: 1080 helix: -1.76 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS q 22 TYR 0.005 0.001 TYR L 8 ARG 0.005 0.001 ARG P 10 *********************** 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 556 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 549 time to evaluate : 0.924 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 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: B 1 GLN cc_start: 0.7938 (tp40) cc_final: 0.7645 (tp40) REVERT: C 17 LYS cc_start: 0.9557 (mptt) cc_final: 0.9279 (mmtm) REVERT: D 13 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9006 (mt-10) REVERT: A 1 GLN cc_start: 0.7463 (tp-100) cc_final: 0.7210 (tp-100) REVERT: E 1 GLN cc_start: 0.7487 (tp40) cc_final: 0.7039 (tp-100) REVERT: H 1 GLN cc_start: 0.7360 (tp40) cc_final: 0.6906 (tp-100) REVERT: L 1 GLN cc_start: 0.7368 (tp40) cc_final: 0.7039 (tp-100) REVERT: L 5 LEU cc_start: 0.9711 (mt) cc_final: 0.9464 (mt) REVERT: O 17 LYS cc_start: 0.9480 (mptt) cc_final: 0.9165 (mmtt) REVERT: P 17 LYS cc_start: 0.9521 (mptt) cc_final: 0.8963 (mmtt) REVERT: P 20 GLU cc_start: 0.9059 (pp20) cc_final: 0.8845 (pp20) REVERT: Q 5 LEU cc_start: 0.9669 (mt) cc_final: 0.9236 (mt) REVERT: Q 18 ILE cc_start: 0.9327 (mt) cc_final: 0.9126 (mt) REVERT: S 17 LYS cc_start: 0.9507 (mptt) cc_final: 0.9124 (mmtt) REVERT: T 5 LEU cc_start: 0.9597 (mt) cc_final: 0.9219 (mp) REVERT: a 1 GLN cc_start: 0.7947 (tp40) cc_final: 0.7656 (tp40) REVERT: d 17 LYS cc_start: 0.9456 (mptt) cc_final: 0.9158 (mmtt) REVERT: f 3 GLU cc_start: 0.9029 (tt0) cc_final: 0.8750 (tp30) REVERT: g 13 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8850 (mt-10) REVERT: h 5 LEU cc_start: 0.9610 (mt) cc_final: 0.9322 (mt) REVERT: h 17 LYS cc_start: 0.9453 (mptt) cc_final: 0.8889 (mmtp) REVERT: h 20 GLU cc_start: 0.9116 (pp20) cc_final: 0.8864 (pp20) REVERT: i 1 GLN cc_start: 0.7416 (tp40) cc_final: 0.7185 (tp40) REVERT: i 13 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8746 (tm-30) REVERT: i 17 LYS cc_start: 0.9479 (mptt) cc_final: 0.8722 (mmmm) REVERT: j 17 LYS cc_start: 0.9535 (mptt) cc_final: 0.9164 (mmtp) REVERT: k 13 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8782 (tm-30) REVERT: k 17 LYS cc_start: 0.9489 (mptt) cc_final: 0.8709 (mmmm) REVERT: l 1 GLN cc_start: 0.7216 (tp-100) cc_final: 0.6896 (tp40) REVERT: m 3 GLU cc_start: 0.9050 (tt0) cc_final: 0.8820 (tp30) REVERT: m 17 LYS cc_start: 0.9519 (mptt) cc_final: 0.9086 (mmtm) REVERT: n 17 LYS cc_start: 0.9457 (mptt) cc_final: 0.8961 (mmtm) REVERT: n 20 GLU cc_start: 0.9049 (pp20) cc_final: 0.8814 (pp20) REVERT: p 20 GLU cc_start: 0.9051 (pp20) cc_final: 0.8841 (pp20) REVERT: q 1 GLN cc_start: 0.6955 (tp40) cc_final: 0.6475 (tp40) REVERT: q 5 LEU cc_start: 0.9362 (mp) cc_final: 0.9150 (mp) REVERT: r 3 GLU cc_start: 0.8700 (tt0) cc_final: 0.8340 (tp30) REVERT: r 17 LYS cc_start: 0.9505 (mptt) cc_final: 0.9092 (mmtt) REVERT: r 20 GLU cc_start: 0.9104 (pp20) cc_final: 0.8892 (pp20) REVERT: r 24 GLU cc_start: 0.9232 (tp30) cc_final: 0.8922 (tm-30) REVERT: r 26 LEU cc_start: 0.9035 (mp) cc_final: 0.8629 (tp) REVERT: s 17 LYS cc_start: 0.9490 (mptt) cc_final: 0.9035 (mmtp) REVERT: t 1 GLN cc_start: 0.8357 (mt0) cc_final: 0.8135 (tp40) REVERT: t 17 LYS cc_start: 0.9497 (mptt) cc_final: 0.9094 (mmtt) REVERT: t 20 GLU cc_start: 0.9056 (pp20) cc_final: 0.8834 (pp20) REVERT: t 24 GLU cc_start: 0.9235 (tp30) cc_final: 0.8896 (tm-30) REVERT: t 26 LEU cc_start: 0.9058 (mp) cc_final: 0.8649 (tp) outliers start: 7 outliers final: 2 residues processed: 549 average time/residue: 0.2314 time to fit residues: 173.1432 Evaluate side-chains 284 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 282 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036435 restraints weight = 59144.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037699 restraints weight = 29657.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.038529 restraints weight = 17903.510| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9180 Z= 0.235 Angle : 0.658 4.994 12320 Z= 0.386 Chirality : 0.042 0.142 1460 Planarity : 0.003 0.025 1600 Dihedral : 5.658 37.383 1280 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.85 % Allowed : 4.02 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.22), residues: 1080 helix: -1.44 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS r 22 TYR 0.005 0.001 TYR A 8 ARG 0.003 0.000 ARG b 6 *********************** 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 548 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 541 time to evaluate : 0.978 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 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: B 1 GLN cc_start: 0.7617 (tp40) cc_final: 0.7219 (tp40) REVERT: C 17 LYS cc_start: 0.9537 (mptt) cc_final: 0.9080 (mmtm) REVERT: D 13 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9019 (mt-10) REVERT: E 1 GLN cc_start: 0.7354 (tp40) cc_final: 0.7046 (tp40) REVERT: E 20 GLU cc_start: 0.9143 (pp20) cc_final: 0.8909 (pp20) REVERT: F 20 GLU cc_start: 0.9023 (pp20) cc_final: 0.8817 (pp20) REVERT: H 1 GLN cc_start: 0.7219 (tp40) cc_final: 0.6815 (tp-100) REVERT: H 20 GLU cc_start: 0.9184 (pp20) cc_final: 0.8943 (pp20) REVERT: L 1 GLN cc_start: 0.7480 (tp40) cc_final: 0.7175 (tp40) REVERT: L 5 LEU cc_start: 0.9706 (mt) cc_final: 0.9471 (mt) REVERT: O 17 LYS cc_start: 0.9530 (mptt) cc_final: 0.9188 (mmtt) REVERT: P 17 LYS cc_start: 0.9524 (mptt) cc_final: 0.9001 (mmtt) REVERT: P 20 GLU cc_start: 0.8851 (pp20) cc_final: 0.8609 (pp20) REVERT: Q 5 LEU cc_start: 0.9646 (mt) cc_final: 0.9397 (mt) REVERT: R 17 LYS cc_start: 0.9623 (mmtt) cc_final: 0.9237 (mmtm) REVERT: T 5 LEU cc_start: 0.9615 (mt) cc_final: 0.9339 (mp) REVERT: T 20 GLU cc_start: 0.9021 (pp20) cc_final: 0.8783 (pp20) REVERT: c 13 GLU cc_start: 0.9200 (mp0) cc_final: 0.8816 (mp0) REVERT: c 17 LYS cc_start: 0.9502 (mptt) cc_final: 0.9051 (mmtp) REVERT: d 13 GLU cc_start: 0.9113 (mp0) cc_final: 0.8759 (mp0) REVERT: d 17 LYS cc_start: 0.9450 (mptt) cc_final: 0.9055 (mmtt) REVERT: e 1 GLN cc_start: 0.8598 (tp40) cc_final: 0.8362 (tp40) REVERT: e 27 LYS cc_start: 0.9285 (tmtt) cc_final: 0.9071 (ttmt) REVERT: f 3 GLU cc_start: 0.9033 (tt0) cc_final: 0.8752 (tp30) REVERT: f 13 GLU cc_start: 0.9050 (mp0) cc_final: 0.8717 (mp0) REVERT: f 17 LYS cc_start: 0.9577 (mptt) cc_final: 0.9072 (mmtt) REVERT: g 13 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8758 (mt-10) REVERT: h 12 LEU cc_start: 0.9505 (mm) cc_final: 0.9224 (tp) REVERT: h 17 LYS cc_start: 0.9437 (mptt) cc_final: 0.8908 (mmtp) REVERT: h 20 GLU cc_start: 0.9145 (pp20) cc_final: 0.8857 (pp20) REVERT: i 1 GLN cc_start: 0.7497 (tp40) cc_final: 0.7264 (tp40) REVERT: i 13 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8759 (tm-30) REVERT: i 17 LYS cc_start: 0.9471 (mptt) cc_final: 0.8686 (mmmm) REVERT: i 24 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9095 (tm-30) REVERT: k 13 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8772 (tm-30) REVERT: k 17 LYS cc_start: 0.9479 (mptt) cc_final: 0.8723 (mmmm) REVERT: l 1 GLN cc_start: 0.7070 (tp-100) cc_final: 0.6749 (tp-100) REVERT: l 18 ILE cc_start: 0.9201 (mp) cc_final: 0.8974 (mp) REVERT: m 3 GLU cc_start: 0.9023 (tt0) cc_final: 0.8783 (tp30) REVERT: n 17 LYS cc_start: 0.9473 (mptt) cc_final: 0.8998 (mmtm) REVERT: n 20 GLU cc_start: 0.8903 (pp20) cc_final: 0.8638 (pp20) REVERT: p 20 GLU cc_start: 0.8887 (pp20) cc_final: 0.8616 (pp20) REVERT: q 1 GLN cc_start: 0.7147 (tp40) cc_final: 0.6731 (tp40) REVERT: q 3 GLU cc_start: 0.9186 (pm20) cc_final: 0.8887 (pm20) REVERT: r 3 GLU cc_start: 0.8723 (tt0) cc_final: 0.8375 (tp30) REVERT: r 17 LYS cc_start: 0.9519 (mptt) cc_final: 0.9084 (mmtt) REVERT: r 20 GLU cc_start: 0.9131 (pp20) cc_final: 0.8867 (pp20) REVERT: r 24 GLU cc_start: 0.9292 (tp30) cc_final: 0.8978 (tm-30) REVERT: r 26 LEU cc_start: 0.9048 (mp) cc_final: 0.8671 (tp) REVERT: s 17 LYS cc_start: 0.9454 (mptt) cc_final: 0.9184 (mmtp) REVERT: t 1 GLN cc_start: 0.8509 (mt0) cc_final: 0.8148 (tp-100) REVERT: t 3 GLU cc_start: 0.9199 (pm20) cc_final: 0.8995 (pm20) REVERT: t 5 LEU cc_start: 0.9465 (mt) cc_final: 0.9176 (mt) REVERT: t 17 LYS cc_start: 0.9497 (mptt) cc_final: 0.9119 (mmtt) REVERT: t 20 GLU cc_start: 0.9054 (pp20) cc_final: 0.8821 (pp20) REVERT: t 24 GLU cc_start: 0.9282 (tp30) cc_final: 0.8944 (tm-30) REVERT: t 26 LEU cc_start: 0.9045 (mp) cc_final: 0.8677 (tp) outliers start: 7 outliers final: 3 residues processed: 541 average time/residue: 0.2228 time to fit residues: 160.7026 Evaluate side-chains 300 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 65 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- 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** ** S 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 = 0.3130 r_free = 0.3130 target = 0.043685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.038467 restraints weight = 56871.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039790 restraints weight = 28246.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040670 restraints weight = 16961.752| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9180 Z= 0.215 Angle : 0.660 5.226 12320 Z= 0.383 Chirality : 0.041 0.146 1460 Planarity : 0.003 0.021 1600 Dihedral : 5.541 28.617 1280 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 1080 helix: -1.12 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS s 22 TYR 0.006 0.001 TYR A 8 ARG 0.003 0.000 ARG n 10 *********************** 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 542 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.989 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 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: B 1 GLN cc_start: 0.8027 (tp40) cc_final: 0.7794 (tp40) REVERT: D 13 GLU cc_start: 0.9309 (mt-10) cc_final: 0.9031 (mt-10) REVERT: A 1 GLN cc_start: 0.7998 (tp40) cc_final: 0.7647 (tp40) REVERT: E 1 GLN cc_start: 0.7294 (tp40) cc_final: 0.7051 (tp40) REVERT: E 20 GLU cc_start: 0.9020 (pp20) cc_final: 0.8773 (pp20) REVERT: F 20 GLU cc_start: 0.9050 (pp20) cc_final: 0.8839 (pp20) REVERT: H 1 GLN cc_start: 0.7204 (tp40) cc_final: 0.6765 (tp-100) REVERT: H 20 GLU cc_start: 0.9133 (pp20) cc_final: 0.8895 (pp20) REVERT: I 1 GLN cc_start: 0.7100 (tp-100) cc_final: 0.6765 (tp-100) REVERT: L 1 GLN cc_start: 0.7481 (tp40) cc_final: 0.7200 (tp40) REVERT: O 17 LYS cc_start: 0.9514 (mptt) cc_final: 0.9007 (mmtm) REVERT: P 17 LYS cc_start: 0.9508 (mptt) cc_final: 0.9030 (mmtt) REVERT: R 17 LYS cc_start: 0.9637 (mmtt) cc_final: 0.9346 (mmtm) REVERT: T 5 LEU cc_start: 0.9594 (mt) cc_final: 0.9362 (mp) REVERT: b 13 GLU cc_start: 0.9122 (pm20) cc_final: 0.8833 (mp0) REVERT: b 17 LYS cc_start: 0.9459 (mptt) cc_final: 0.9153 (mmtt) REVERT: c 13 GLU cc_start: 0.9150 (mp0) cc_final: 0.8918 (mp0) REVERT: c 17 LYS cc_start: 0.9562 (mptt) cc_final: 0.9293 (mmtt) REVERT: d 13 GLU cc_start: 0.9092 (mp0) cc_final: 0.8838 (mp0) REVERT: d 17 LYS cc_start: 0.9466 (mptt) cc_final: 0.9069 (mmtt) REVERT: e 1 GLN cc_start: 0.8609 (tp40) cc_final: 0.8340 (tp40) REVERT: f 3 GLU cc_start: 0.8988 (tt0) cc_final: 0.8764 (tp30) REVERT: g 13 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8707 (mt-10) REVERT: h 17 LYS cc_start: 0.9442 (mptt) cc_final: 0.8870 (mmtt) REVERT: h 20 GLU cc_start: 0.9107 (pp20) cc_final: 0.8804 (pp20) REVERT: i 1 GLN cc_start: 0.7598 (tp40) cc_final: 0.7359 (tp-100) REVERT: i 13 GLU cc_start: 0.9352 (mt-10) cc_final: 0.8724 (tm-30) REVERT: i 17 LYS cc_start: 0.9500 (mptt) cc_final: 0.8956 (mmmm) REVERT: k 13 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8803 (tm-30) REVERT: k 17 LYS cc_start: 0.9509 (mptt) cc_final: 0.9085 (mmmm) REVERT: l 1 GLN cc_start: 0.7103 (tp-100) cc_final: 0.6762 (tp-100) REVERT: m 17 LYS cc_start: 0.9554 (mptt) cc_final: 0.9015 (mmmm) REVERT: n 12 LEU cc_start: 0.9606 (mm) cc_final: 0.9283 (tp) REVERT: n 17 LYS cc_start: 0.9455 (mptt) cc_final: 0.9007 (mmtm) REVERT: p 12 LEU cc_start: 0.9588 (mm) cc_final: 0.9285 (tp) REVERT: r 4 ILE cc_start: 0.9621 (mt) cc_final: 0.8933 (mt) REVERT: r 15 ASP cc_start: 0.9385 (m-30) cc_final: 0.9168 (m-30) REVERT: r 17 LYS cc_start: 0.9514 (mptt) cc_final: 0.9106 (mmtt) REVERT: r 18 ILE cc_start: 0.9251 (mt) cc_final: 0.8993 (mt) REVERT: r 20 GLU cc_start: 0.9147 (pp20) cc_final: 0.8861 (pp20) REVERT: r 24 GLU cc_start: 0.9282 (tp30) cc_final: 0.8996 (tm-30) REVERT: r 26 LEU cc_start: 0.9007 (mp) cc_final: 0.8661 (tp) REVERT: t 1 GLN cc_start: 0.8485 (mt0) cc_final: 0.8151 (tp-100) REVERT: t 3 GLU cc_start: 0.9193 (pm20) cc_final: 0.8987 (pm20) REVERT: t 5 LEU cc_start: 0.9442 (mt) cc_final: 0.9197 (mt) REVERT: t 17 LYS cc_start: 0.9506 (mptt) cc_final: 0.9123 (mmtt) REVERT: t 18 ILE cc_start: 0.9245 (mt) cc_final: 0.8993 (mt) REVERT: t 20 GLU cc_start: 0.9001 (pp20) cc_final: 0.8784 (pp20) REVERT: t 24 GLU cc_start: 0.9250 (tp30) cc_final: 0.8948 (tm-30) REVERT: t 26 LEU cc_start: 0.9007 (mp) cc_final: 0.8664 (tp) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.2226 time to fit residues: 160.8143 Evaluate side-chains 290 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 1 GLN ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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 = 0.3154 r_free = 0.3154 target = 0.044069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038798 restraints weight = 57597.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040144 restraints weight = 28718.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.041032 restraints weight = 17197.333| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9180 Z= 0.219 Angle : 0.701 5.655 12320 Z= 0.405 Chirality : 0.041 0.153 1460 Planarity : 0.003 0.020 1600 Dihedral : 5.479 31.584 1280 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.23), residues: 1080 helix: -0.95 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS r 22 TYR 0.006 0.001 TYR C 8 ARG 0.004 0.000 ARG s 10 *********************** 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 539 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 0.975 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 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: B 1 GLN cc_start: 0.8264 (tp40) cc_final: 0.8059 (tp40) REVERT: A 1 GLN cc_start: 0.8243 (tp40) cc_final: 0.7831 (tp40) REVERT: E 20 GLU cc_start: 0.8989 (pp20) cc_final: 0.8754 (pp20) REVERT: H 1 GLN cc_start: 0.7221 (tp40) cc_final: 0.6844 (tp-100) REVERT: P 17 LYS cc_start: 0.9482 (mptt) cc_final: 0.8954 (mmtm) REVERT: S 12 LEU cc_start: 0.9559 (mm) cc_final: 0.9292 (tp) REVERT: b 17 LYS cc_start: 0.9508 (mptt) cc_final: 0.9137 (mmtt) REVERT: c 13 GLU cc_start: 0.9191 (mp0) cc_final: 0.8783 (mp0) REVERT: c 17 LYS cc_start: 0.9573 (mptt) cc_final: 0.9275 (mmtt) REVERT: c 18 ILE cc_start: 0.9247 (mt) cc_final: 0.9013 (mt) REVERT: d 13 GLU cc_start: 0.9120 (mp0) cc_final: 0.8736 (mp0) REVERT: d 17 LYS cc_start: 0.9427 (mptt) cc_final: 0.9095 (mmtt) REVERT: e 1 GLN cc_start: 0.8708 (tp40) cc_final: 0.8325 (tp40) REVERT: f 3 GLU cc_start: 0.8926 (tt0) cc_final: 0.8684 (tp30) REVERT: f 13 GLU cc_start: 0.9050 (mp0) cc_final: 0.8685 (mp0) REVERT: f 17 LYS cc_start: 0.9502 (mptt) cc_final: 0.9080 (mmtp) REVERT: f 20 GLU cc_start: 0.9064 (pp20) cc_final: 0.8863 (pp20) REVERT: g 13 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8678 (mt-10) REVERT: h 12 LEU cc_start: 0.9438 (mm) cc_final: 0.9195 (tp) REVERT: i 13 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8695 (tm-30) REVERT: i 17 LYS cc_start: 0.9506 (mptt) cc_final: 0.8936 (mmmm) REVERT: k 13 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8785 (tm-30) REVERT: k 17 LYS cc_start: 0.9493 (mptt) cc_final: 0.8971 (mmmm) REVERT: l 1 GLN cc_start: 0.6904 (tp-100) cc_final: 0.6602 (tp-100) REVERT: m 17 LYS cc_start: 0.9417 (mptt) cc_final: 0.8953 (mmmm) REVERT: n 12 LEU cc_start: 0.9548 (mm) cc_final: 0.9234 (tp) REVERT: n 17 LYS cc_start: 0.9445 (mptt) cc_final: 0.8998 (mmtm) REVERT: o 17 LYS cc_start: 0.9481 (mptt) cc_final: 0.9060 (mmmm) REVERT: p 12 LEU cc_start: 0.9527 (mm) cc_final: 0.9222 (tp) REVERT: p 17 LYS cc_start: 0.9418 (mptt) cc_final: 0.8942 (mmtm) REVERT: p 20 GLU cc_start: 0.8726 (pp20) cc_final: 0.8481 (pp20) REVERT: r 4 ILE cc_start: 0.9499 (mt) cc_final: 0.9078 (mt) REVERT: r 15 ASP cc_start: 0.9393 (m-30) cc_final: 0.9183 (m-30) REVERT: r 17 LYS cc_start: 0.9447 (mptt) cc_final: 0.9067 (mmtt) REVERT: r 18 ILE cc_start: 0.9234 (mt) cc_final: 0.8998 (mt) REVERT: r 20 GLU cc_start: 0.9000 (pp20) cc_final: 0.8758 (pp20) REVERT: r 24 GLU cc_start: 0.9133 (tp30) cc_final: 0.8927 (tm-30) REVERT: r 26 LEU cc_start: 0.8977 (mp) cc_final: 0.8633 (tp) REVERT: t 17 LYS cc_start: 0.9466 (mptt) cc_final: 0.9088 (mmtt) REVERT: t 18 ILE cc_start: 0.9235 (mt) cc_final: 0.9034 (mt) REVERT: t 24 GLU cc_start: 0.9141 (tp30) cc_final: 0.8922 (tm-30) REVERT: t 26 LEU cc_start: 0.8971 (mp) cc_final: 0.8630 (tp) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.2275 time to fit residues: 164.4982 Evaluate side-chains 303 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 GLN ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.041955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.036887 restraints weight = 58976.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038160 restraints weight = 29241.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.039000 restraints weight = 17594.337| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9180 Z= 0.300 Angle : 0.776 5.958 12320 Z= 0.451 Chirality : 0.045 0.173 1460 Planarity : 0.004 0.030 1600 Dihedral : 5.783 41.968 1280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1080 helix: -1.02 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 22 TYR 0.007 0.001 TYR e 8 ARG 0.002 0.000 ARG b 6 *********************** 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 527 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.985 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: A 1 GLN cc_start: 0.8454 (tp40) cc_final: 0.8160 (tp40) REVERT: E 29 GLN cc_start: 0.8784 (tt0) cc_final: 0.8458 (tt0) REVERT: F 11 ILE cc_start: 0.9398 (pt) cc_final: 0.9177 (pt) REVERT: H 1 GLN cc_start: 0.7207 (tp40) cc_final: 0.6835 (tp-100) REVERT: M 3 GLU cc_start: 0.9362 (pm20) cc_final: 0.9146 (pm20) REVERT: O 12 LEU cc_start: 0.9494 (mm) cc_final: 0.9201 (tp) REVERT: P 12 LEU cc_start: 0.9421 (mm) cc_final: 0.9197 (tt) REVERT: P 17 LYS cc_start: 0.9563 (mptt) cc_final: 0.9053 (mmtm) REVERT: P 20 GLU cc_start: 0.9150 (pp20) cc_final: 0.8900 (pp20) REVERT: S 12 LEU cc_start: 0.9601 (mm) cc_final: 0.9336 (tp) REVERT: T 20 GLU cc_start: 0.8994 (pp20) cc_final: 0.8752 (pp20) REVERT: a 13 GLU cc_start: 0.9231 (pm20) cc_final: 0.8988 (mp0) REVERT: a 17 LYS cc_start: 0.9492 (mptt) cc_final: 0.9235 (mmtp) REVERT: c 18 ILE cc_start: 0.9319 (mt) cc_final: 0.9118 (mt) REVERT: d 13 GLU cc_start: 0.9083 (mp0) cc_final: 0.8794 (mp0) REVERT: d 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.9079 (mmtt) REVERT: e 3 GLU cc_start: 0.9009 (pm20) cc_final: 0.8778 (pm20) REVERT: e 17 LYS cc_start: 0.9478 (mptt) cc_final: 0.9145 (mmtp) REVERT: f 3 GLU cc_start: 0.8940 (tt0) cc_final: 0.8694 (tp30) REVERT: f 20 GLU cc_start: 0.9133 (pp20) cc_final: 0.8891 (pp20) REVERT: g 13 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8735 (mp0) REVERT: h 12 LEU cc_start: 0.9492 (mm) cc_final: 0.9235 (tp) REVERT: h 17 LYS cc_start: 0.9413 (mmtp) cc_final: 0.8768 (mptt) REVERT: h 18 ILE cc_start: 0.9397 (mt) cc_final: 0.9164 (mt) REVERT: h 20 GLU cc_start: 0.9119 (pp20) cc_final: 0.8818 (pp20) REVERT: i 1 GLN cc_start: 0.8373 (tp40) cc_final: 0.8147 (tp40) REVERT: l 1 GLN cc_start: 0.6890 (tp-100) cc_final: 0.6586 (tp-100) REVERT: l 5 LEU cc_start: 0.9739 (mt) cc_final: 0.9514 (mt) REVERT: n 12 LEU cc_start: 0.9587 (mm) cc_final: 0.9275 (tp) REVERT: n 17 LYS cc_start: 0.9509 (mptt) cc_final: 0.9040 (mmtm) REVERT: n 20 GLU cc_start: 0.9107 (pp20) cc_final: 0.8883 (pp20) REVERT: o 17 LYS cc_start: 0.9472 (mptt) cc_final: 0.9120 (mmmm) REVERT: p 12 LEU cc_start: 0.9572 (mm) cc_final: 0.9256 (tp) REVERT: p 17 LYS cc_start: 0.9505 (mptt) cc_final: 0.9022 (mmtm) REVERT: q 13 GLU cc_start: 0.9273 (pm20) cc_final: 0.8980 (mp0) REVERT: q 17 LYS cc_start: 0.9515 (mptt) cc_final: 0.9207 (mmtp) REVERT: r 15 ASP cc_start: 0.9449 (m-30) cc_final: 0.9237 (m-30) REVERT: r 17 LYS cc_start: 0.9467 (mptt) cc_final: 0.9081 (mmtt) REVERT: r 18 ILE cc_start: 0.9254 (mt) cc_final: 0.9049 (mt) REVERT: r 20 GLU cc_start: 0.9086 (pp20) cc_final: 0.8764 (pp20) REVERT: r 24 GLU cc_start: 0.9259 (tp30) cc_final: 0.9011 (tm-30) REVERT: r 26 LEU cc_start: 0.9036 (mp) cc_final: 0.8712 (tp) REVERT: t 15 ASP cc_start: 0.9438 (m-30) cc_final: 0.9232 (m-30) REVERT: t 17 LYS cc_start: 0.9483 (mptt) cc_final: 0.9109 (mmtt) REVERT: t 18 ILE cc_start: 0.9258 (mt) cc_final: 0.9044 (mt) REVERT: t 20 GLU cc_start: 0.9030 (pp20) cc_final: 0.8790 (pp20) REVERT: t 24 GLU cc_start: 0.9269 (tp30) cc_final: 0.9004 (tm-30) REVERT: t 26 LEU cc_start: 0.9023 (mp) cc_final: 0.8706 (tp) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.2215 time to fit residues: 155.5024 Evaluate side-chains 297 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 77 optimal weight: 0.0470 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 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 = 0.3124 r_free = 0.3124 target = 0.043056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037901 restraints weight = 59251.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039219 restraints weight = 29890.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040111 restraints weight = 18028.924| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.6253 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= 0.268 Angle : 0.827 6.409 12320 Z= 0.478 Chirality : 0.044 0.170 1460 Planarity : 0.003 0.022 1600 Dihedral : 5.729 37.130 1280 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1080 helix: -0.80 (0.14), residues: 1060 sheet: None (None), residues: 0 loop : 8.95 (0.93), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS m 22 TYR 0.009 0.001 TYR A 8 ARG 0.002 0.000 ARG t 6 *********************** 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 530 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 1.094 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: A 1 GLN cc_start: 0.8552 (tp40) cc_final: 0.8284 (tp40) REVERT: E 1 GLN cc_start: 0.7132 (tp40) cc_final: 0.6863 (tp-100) REVERT: E 20 GLU cc_start: 0.9132 (pp20) cc_final: 0.8931 (pp20) REVERT: F 13 GLU cc_start: 0.9033 (mp0) cc_final: 0.8405 (mp0) REVERT: F 17 LYS cc_start: 0.9454 (mptt) cc_final: 0.9020 (mmtt) REVERT: H 1 GLN cc_start: 0.7257 (tp40) cc_final: 0.6791 (tp-100) REVERT: H 20 GLU cc_start: 0.9097 (pp20) cc_final: 0.8853 (pp20) REVERT: L 1 GLN cc_start: 0.7607 (tp40) cc_final: 0.7330 (tp40) REVERT: O 12 LEU cc_start: 0.9461 (mm) cc_final: 0.9150 (tp) REVERT: O 17 LYS cc_start: 0.9472 (mptt) cc_final: 0.8972 (mmtm) REVERT: P 12 LEU cc_start: 0.9445 (mm) cc_final: 0.9238 (tp) REVERT: P 17 LYS cc_start: 0.9490 (mptt) cc_final: 0.9037 (mmtm) REVERT: P 20 GLU cc_start: 0.9047 (pp20) cc_final: 0.8808 (pp20) REVERT: S 12 LEU cc_start: 0.9564 (mm) cc_final: 0.9300 (tp) REVERT: a 13 GLU cc_start: 0.9188 (pm20) cc_final: 0.8939 (mp0) REVERT: a 17 LYS cc_start: 0.9615 (mptt) cc_final: 0.9337 (mmtt) REVERT: b 13 GLU cc_start: 0.9200 (pm20) cc_final: 0.8859 (pm20) REVERT: b 17 LYS cc_start: 0.9438 (mptt) cc_final: 0.9034 (mmtt) REVERT: d 13 GLU cc_start: 0.9037 (mp0) cc_final: 0.8737 (mp0) REVERT: d 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.9119 (mmtt) REVERT: e 3 GLU cc_start: 0.9016 (pm20) cc_final: 0.8768 (pm20) REVERT: f 3 GLU cc_start: 0.8914 (tt0) cc_final: 0.8673 (tp30) REVERT: f 13 GLU cc_start: 0.9143 (mp0) cc_final: 0.8741 (mp0) REVERT: f 17 LYS cc_start: 0.9480 (mptt) cc_final: 0.9058 (mmtt) REVERT: f 20 GLU cc_start: 0.9022 (pp20) cc_final: 0.8785 (pp20) REVERT: g 13 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8736 (mp0) REVERT: g 27 LYS cc_start: 0.9218 (tmtt) cc_final: 0.9000 (ttmt) REVERT: h 12 LEU cc_start: 0.9507 (mm) cc_final: 0.9304 (tp) REVERT: h 20 GLU cc_start: 0.9068 (pp20) cc_final: 0.8794 (pp20) REVERT: i 1 GLN cc_start: 0.8402 (tp40) cc_final: 0.8195 (tp40) REVERT: i 13 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8837 (tm-30) REVERT: i 17 LYS cc_start: 0.9508 (mptt) cc_final: 0.9138 (mmmm) REVERT: j 17 LYS cc_start: 0.9607 (mptt) cc_final: 0.9228 (mmtp) REVERT: k 13 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8919 (tm-30) REVERT: k 17 LYS cc_start: 0.9515 (mptt) cc_final: 0.9168 (mmmm) REVERT: k 20 GLU cc_start: 0.9090 (pm20) cc_final: 0.8888 (pm20) REVERT: l 1 GLN cc_start: 0.6870 (tp-100) cc_final: 0.6573 (tp-100) REVERT: n 12 LEU cc_start: 0.9553 (mm) cc_final: 0.9210 (tp) REVERT: n 17 LYS cc_start: 0.9461 (mptt) cc_final: 0.8977 (mmtm) REVERT: n 20 GLU cc_start: 0.9045 (pp20) cc_final: 0.8823 (pp20) REVERT: o 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.9095 (mmmm) REVERT: p 1 GLN cc_start: 0.8633 (tp40) cc_final: 0.8388 (tm-30) REVERT: q 13 GLU cc_start: 0.9217 (pm20) cc_final: 0.8819 (mp0) REVERT: q 17 LYS cc_start: 0.9510 (mptt) cc_final: 0.9219 (mmtp) REVERT: r 17 LYS cc_start: 0.9485 (mptt) cc_final: 0.9144 (mmtt) REVERT: r 18 ILE cc_start: 0.9238 (mt) cc_final: 0.9036 (mt) REVERT: r 20 GLU cc_start: 0.9029 (pp20) cc_final: 0.8749 (pp20) REVERT: r 26 LEU cc_start: 0.9005 (mp) cc_final: 0.8701 (tp) REVERT: t 17 LYS cc_start: 0.9448 (mptt) cc_final: 0.9124 (mmtt) REVERT: t 20 GLU cc_start: 0.8964 (pp20) cc_final: 0.8704 (pp20) REVERT: t 24 GLU cc_start: 0.9227 (tp30) cc_final: 0.8988 (tm-30) REVERT: t 26 LEU cc_start: 0.9004 (mp) cc_final: 0.8689 (tp) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.2478 time to fit residues: 177.0368 Evaluate side-chains 299 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 0.0060 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 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 = 0.3142 r_free = 0.3142 target = 0.043622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.038315 restraints weight = 56832.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039650 restraints weight = 28148.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.040550 restraints weight = 16922.875| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9180 Z= 0.268 Angle : 0.851 7.216 12320 Z= 0.487 Chirality : 0.044 0.187 1460 Planarity : 0.003 0.017 1600 Dihedral : 5.577 32.015 1280 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1080 helix: -0.67 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : 8.51 (0.93), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS r 22 TYR 0.010 0.001 TYR A 8 ARG 0.002 0.000 ARG n 10 ********************** 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 535 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 0.997 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 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: A 1 GLN cc_start: 0.8505 (tp40) cc_final: 0.8112 (tm-30) REVERT: F 13 GLU cc_start: 0.8934 (mp0) cc_final: 0.8410 (mp0) REVERT: F 17 LYS cc_start: 0.9455 (mptt) cc_final: 0.9028 (mmtt) REVERT: H 1 GLN cc_start: 0.7400 (tp40) cc_final: 0.6892 (tp-100) REVERT: H 20 GLU cc_start: 0.9091 (pp20) cc_final: 0.8843 (pp20) REVERT: I 1 GLN cc_start: 0.8236 (tp40) cc_final: 0.8021 (tp40) REVERT: J 13 GLU cc_start: 0.9142 (pm20) cc_final: 0.8925 (pm20) REVERT: J 17 LYS cc_start: 0.9543 (mptt) cc_final: 0.8934 (mmtp) REVERT: L 1 GLN cc_start: 0.7698 (tp40) cc_final: 0.7459 (tp40) REVERT: N 12 LEU cc_start: 0.9408 (mm) cc_final: 0.9163 (mm) REVERT: N 13 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8866 (mt-10) REVERT: N 15 ASP cc_start: 0.9016 (m-30) cc_final: 0.8646 (t0) REVERT: O 17 LYS cc_start: 0.9504 (mptt) cc_final: 0.9011 (mmtt) REVERT: P 12 LEU cc_start: 0.9451 (mm) cc_final: 0.9190 (tp) REVERT: P 17 LYS cc_start: 0.9531 (mptt) cc_final: 0.9052 (mmtm) REVERT: P 20 GLU cc_start: 0.9018 (pp20) cc_final: 0.8757 (pp20) REVERT: S 12 LEU cc_start: 0.9569 (mm) cc_final: 0.9307 (tp) REVERT: S 27 LYS cc_start: 0.9011 (tmtt) cc_final: 0.8613 (ttmm) REVERT: a 13 GLU cc_start: 0.9198 (pm20) cc_final: 0.8898 (mp0) REVERT: a 17 LYS cc_start: 0.9607 (mptt) cc_final: 0.9342 (mmtt) REVERT: d 1 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8208 (tm-30) REVERT: e 3 GLU cc_start: 0.8996 (pm20) cc_final: 0.8727 (pm20) REVERT: f 3 GLU cc_start: 0.8925 (tt0) cc_final: 0.8588 (tp30) REVERT: f 13 GLU cc_start: 0.9128 (mp0) cc_final: 0.8769 (mp0) REVERT: f 17 LYS cc_start: 0.9463 (mptt) cc_final: 0.9045 (mmtt) REVERT: f 20 GLU cc_start: 0.9030 (pp20) cc_final: 0.8802 (pp20) REVERT: g 13 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8663 (mp0) REVERT: h 20 GLU cc_start: 0.9032 (pp20) cc_final: 0.8741 (pp20) REVERT: i 1 GLN cc_start: 0.8503 (tp40) cc_final: 0.8286 (tp40) REVERT: i 13 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8815 (tm-30) REVERT: i 17 LYS cc_start: 0.9515 (mptt) cc_final: 0.9117 (mmmm) REVERT: i 20 GLU cc_start: 0.9042 (pm20) cc_final: 0.8831 (pm20) REVERT: j 17 LYS cc_start: 0.9614 (mptt) cc_final: 0.9181 (mmtp) REVERT: k 13 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8800 (tm-30) REVERT: k 17 LYS cc_start: 0.9515 (mptt) cc_final: 0.8989 (mmmm) REVERT: l 1 GLN cc_start: 0.6818 (tp-100) cc_final: 0.6540 (tp-100) REVERT: m 1 GLN cc_start: 0.8911 (tp40) cc_final: 0.8598 (tm-30) REVERT: n 12 LEU cc_start: 0.9528 (mm) cc_final: 0.9164 (tp) REVERT: n 17 LYS cc_start: 0.9461 (mptt) cc_final: 0.8983 (mmtm) REVERT: n 20 GLU cc_start: 0.9043 (pp20) cc_final: 0.8813 (pp20) REVERT: o 17 LYS cc_start: 0.9472 (mptt) cc_final: 0.9036 (mmmm) REVERT: p 1 GLN cc_start: 0.8644 (tp40) cc_final: 0.8283 (tm-30) REVERT: p 17 LYS cc_start: 0.9539 (mptt) cc_final: 0.9091 (mmtt) REVERT: r 17 LYS cc_start: 0.9479 (mptt) cc_final: 0.9149 (mmtt) REVERT: r 18 ILE cc_start: 0.9190 (mt) cc_final: 0.8977 (mt) REVERT: r 20 GLU cc_start: 0.9023 (pp20) cc_final: 0.8688 (pp20) REVERT: r 26 LEU cc_start: 0.8990 (mp) cc_final: 0.8689 (tp) REVERT: t 17 LYS cc_start: 0.9464 (mptt) cc_final: 0.9120 (mmtt) REVERT: t 20 GLU cc_start: 0.9003 (pp20) cc_final: 0.8725 (pp20) REVERT: t 24 GLU cc_start: 0.9249 (tp30) cc_final: 0.9027 (tm-30) REVERT: t 26 LEU cc_start: 0.9014 (mp) cc_final: 0.8719 (tp) outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.2245 time to fit residues: 160.4532 Evaluate side-chains 321 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3108 r_free = 0.3108 target = 0.042251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036892 restraints weight = 58023.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038195 restraints weight = 29584.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039081 restraints weight = 18153.630| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9180 Z= 0.311 Angle : 0.886 7.260 12320 Z= 0.510 Chirality : 0.048 0.210 1460 Planarity : 0.003 0.024 1600 Dihedral : 5.606 30.262 1280 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1080 helix: -0.75 (0.14), residues: 1060 sheet: None (None), residues: 0 loop : 9.32 (1.20), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS q 22 TYR 0.008 0.001 TYR A 8 ARG 0.002 0.000 ARG g 6 =============================================================================== Job complete usr+sys time: 3487.73 seconds wall clock time: 61 minutes 38.46 seconds (3698.46 seconds total)