Starting phenix.real_space_refine on Thu Feb 13 07:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wky_21813/02_2025/6wky_21813.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wky_21813/02_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_21813/02_2025/6wky_21813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wky_21813/02_2025/6wky_21813.map" model { file = "/net/cci-nas-00/data/ceres_data/6wky_21813/02_2025/6wky_21813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wky_21813/02_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-5592/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: 5.90, per 1000 atoms: 0.65 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: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.71 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: 2.01 Time building geometry restraints manager: 2.50 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.340 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- 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 : 1.122 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: 0.2308 time to fit residues: 186.4103 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 : 1.025 ------------------------------------------------------------------------------- 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 = 0.042046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036811 restraints weight = 55670.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.038068 restraints weight = 28732.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038937 restraints weight = 17760.994| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- 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 : 1.071 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: 0.7304 (tp40) cc_final: 0.6955 (tp40) REVERT: B 3 GLU cc_start: 0.8937 (tt0) cc_final: 0.8704 (tp30) REVERT: B 13 GLU cc_start: 0.9157 (tt0) cc_final: 0.8906 (mt-10) REVERT: A 17 LYS cc_start: 0.9570 (mptt) cc_final: 0.9093 (mmtm) REVERT: E 1 GLN cc_start: 0.7090 (tp40) cc_final: 0.6543 (tp-100) REVERT: F 13 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8537 (mp0) REVERT: F 17 LYS cc_start: 0.9475 (mptt) cc_final: 0.9125 (mmtt) REVERT: F 20 GLU cc_start: 0.9136 (pp20) cc_final: 0.8885 (pp20) REVERT: H 1 GLN cc_start: 0.7347 (tp40) cc_final: 0.7047 (tp40) REVERT: H 20 GLU cc_start: 0.9126 (pp20) cc_final: 0.8879 (pp20) REVERT: I 5 LEU cc_start: 0.9699 (mt) cc_final: 0.9412 (mt) REVERT: I 13 GLU cc_start: 0.9403 (mt-10) cc_final: 0.8841 (mt-10) REVERT: K 13 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8999 (mp0) REVERT: L 1 GLN cc_start: 0.7148 (tp40) cc_final: 0.6745 (tp40) REVERT: L 5 LEU cc_start: 0.9699 (mt) cc_final: 0.9456 (mt) REVERT: L 13 GLU cc_start: 0.9017 (mp0) cc_final: 0.8660 (mp0) REVERT: L 17 LYS cc_start: 0.9435 (mptt) cc_final: 0.8921 (mmtt) REVERT: M 5 LEU cc_start: 0.9767 (mt) cc_final: 0.9235 (mp) REVERT: O 17 LYS cc_start: 0.9562 (mptt) cc_final: 0.9060 (mmtm) REVERT: P 17 LYS cc_start: 0.9614 (mptt) cc_final: 0.9108 (mmtm) REVERT: Q 17 LYS cc_start: 0.9465 (mptt) cc_final: 0.9029 (mmtt) REVERT: T 1 GLN cc_start: 0.7243 (tp40) cc_final: 0.6942 (tp40) REVERT: T 5 LEU cc_start: 0.9684 (mt) cc_final: 0.9437 (mt) REVERT: e 3 GLU cc_start: 0.9113 (tt0) cc_final: 0.8742 (tp30) REVERT: e 17 LYS cc_start: 0.9401 (mptt) cc_final: 0.8966 (mmtt) REVERT: e 27 LYS cc_start: 0.9363 (tptm) cc_final: 0.9030 (mmmt) REVERT: f 3 GLU cc_start: 0.8954 (tt0) cc_final: 0.8750 (tp30) REVERT: f 11 ILE cc_start: 0.9326 (mt) cc_final: 0.9072 (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: 0.8971 (mmtt) REVERT: h 5 LEU cc_start: 0.9486 (mt) cc_final: 0.9199 (mt) REVERT: i 1 GLN cc_start: 0.6962 (tp40) cc_final: 0.6574 (tp-100) REVERT: i 13 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8807 (tm-30) REVERT: i 17 LYS cc_start: 0.9463 (mptt) cc_final: 0.9152 (mmmm) REVERT: k 13 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8790 (tm-30) REVERT: l 1 GLN cc_start: 0.6757 (tp40) cc_final: 0.6467 (tp40) REVERT: l 5 LEU cc_start: 0.9752 (mt) cc_final: 0.9505 (mt) REVERT: m 3 GLU cc_start: 0.9005 (tt0) cc_final: 0.8765 (tp30) REVERT: n 3 GLU cc_start: 0.9007 (tt0) cc_final: 0.8777 (tp30) REVERT: o 13 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8705 (mt-10) REVERT: p 1 GLN cc_start: 0.7394 (tp40) cc_final: 0.7122 (tp40) REVERT: p 3 GLU cc_start: 0.8902 (tt0) cc_final: 0.8629 (tp30) REVERT: q 5 LEU cc_start: 0.9212 (mp) cc_final: 0.9010 (mp) REVERT: q 13 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8533 (mt-10) REVERT: r 3 GLU cc_start: 0.8825 (tt0) cc_final: 0.8576 (tp30) REVERT: r 17 LYS cc_start: 0.9547 (mptt) cc_final: 0.9128 (mmtt) REVERT: r 20 GLU cc_start: 0.9201 (pp20) cc_final: 0.9000 (pp20) REVERT: r 26 LEU cc_start: 0.9046 (mp) cc_final: 0.8497 (tp) REVERT: t 17 LYS cc_start: 0.9521 (mptt) cc_final: 0.9101 (mmtt) REVERT: t 24 GLU cc_start: 0.9260 (tp30) cc_final: 0.9044 (tp30) REVERT: t 26 LEU cc_start: 0.8986 (mp) cc_final: 0.8518 (tp) outliers start: 28 outliers final: 0 residues processed: 586 average time/residue: 0.2270 time to fit residues: 178.2341 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 : 1.082 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 overall best weight: 2.4544 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.043141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037944 restraints weight = 58287.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039267 restraints weight = 29186.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040150 restraints weight = 17662.104| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9180 Z= 0.199 Angle : 0.591 4.632 12320 Z= 0.342 Chirality : 0.039 0.135 1460 Planarity : 0.003 0.036 1600 Dihedral : 5.428 34.054 1280 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.71 % Allowed : 3.90 % Favored : 94.39 % 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: -4.09 (0.20), residues: 1080 helix: -2.38 (0.12), 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 0.008 0.001 TYR f 8 ARG 0.003 0.000 ARG f 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 578 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 564 time to evaluate : 1.042 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: C 17 LYS cc_start: 0.9576 (mptt) cc_final: 0.9187 (mmtm) REVERT: D 13 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9034 (mt-10) REVERT: F 20 GLU cc_start: 0.9110 (pp20) cc_final: 0.8898 (pp20) REVERT: H 1 GLN cc_start: 0.7311 (tp40) cc_final: 0.6928 (tp-100) REVERT: H 20 GLU cc_start: 0.9171 (pp20) cc_final: 0.8959 (pp20) REVERT: I 29 GLN cc_start: 0.8455 (tt0) cc_final: 0.8188 (tm-30) REVERT: J 13 GLU cc_start: 0.8998 (mp0) cc_final: 0.8757 (mp0) REVERT: J 17 LYS cc_start: 0.9481 (mptt) cc_final: 0.9126 (mmtp) REVERT: K 13 GLU cc_start: 0.9402 (mt-10) cc_final: 0.8835 (mt-10) REVERT: L 1 GLN cc_start: 0.7239 (tp40) cc_final: 0.6910 (tp40) REVERT: O 17 LYS cc_start: 0.9493 (mptt) cc_final: 0.9022 (mmtm) REVERT: Q 1 GLN cc_start: 0.7219 (tp40) cc_final: 0.6896 (tp-100) REVERT: Q 5 LEU cc_start: 0.9677 (mt) cc_final: 0.9287 (mt) REVERT: S 17 LYS cc_start: 0.9496 (mptt) cc_final: 0.9129 (mmtt) REVERT: T 5 LEU cc_start: 0.9648 (mt) cc_final: 0.9384 (mp) REVERT: a 3 GLU cc_start: 0.9023 (pm20) cc_final: 0.8789 (pm20) REVERT: a 17 LYS cc_start: 0.9500 (mptt) cc_final: 0.9094 (mmtp) REVERT: e 17 LYS cc_start: 0.9368 (mptt) cc_final: 0.8964 (mmtt) REVERT: f 3 GLU cc_start: 0.8948 (tt0) cc_final: 0.8737 (tp30) REVERT: f 17 LYS cc_start: 0.9617 (mptt) cc_final: 0.9200 (mmtp) REVERT: h 5 LEU cc_start: 0.9631 (mt) cc_final: 0.9262 (mt) REVERT: h 20 GLU cc_start: 0.9118 (pp20) cc_final: 0.8873 (pp20) REVERT: i 1 GLN cc_start: 0.7255 (tp40) cc_final: 0.7053 (tp40) REVERT: i 13 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8790 (tm-30) REVERT: i 17 LYS cc_start: 0.9476 (mptt) cc_final: 0.8725 (mmmm) REVERT: j 17 LYS cc_start: 0.9520 (mptt) cc_final: 0.9213 (mmtp) REVERT: k 13 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8754 (tm-30) REVERT: k 17 LYS cc_start: 0.9461 (mptt) cc_final: 0.8695 (mmmm) REVERT: l 5 LEU cc_start: 0.9756 (mt) cc_final: 0.9484 (mt) REVERT: m 3 GLU cc_start: 0.8980 (tt0) cc_final: 0.8779 (tp30) REVERT: m 11 ILE cc_start: 0.9324 (mt) cc_final: 0.9036 (mt) REVERT: m 17 LYS cc_start: 0.9503 (mptt) cc_final: 0.9120 (mmtm) REVERT: n 20 GLU cc_start: 0.9104 (pp20) cc_final: 0.8871 (pp20) REVERT: p 3 GLU cc_start: 0.8851 (tt0) cc_final: 0.8512 (tp30) REVERT: p 20 GLU cc_start: 0.9056 (pp20) cc_final: 0.8801 (pp20) REVERT: q 1 GLN cc_start: 0.6986 (tp40) cc_final: 0.6488 (tp40) REVERT: q 3 GLU cc_start: 0.9133 (pm20) cc_final: 0.8887 (pm20) REVERT: q 5 LEU cc_start: 0.9372 (mp) cc_final: 0.9125 (mp) REVERT: r 3 GLU cc_start: 0.8716 (tt0) cc_final: 0.8488 (tp30) REVERT: r 17 LYS cc_start: 0.9507 (mptt) cc_final: 0.9084 (mmtt) REVERT: r 20 GLU cc_start: 0.9113 (pp20) cc_final: 0.8904 (pp20) REVERT: r 24 GLU cc_start: 0.9213 (tp30) cc_final: 0.8901 (tm-30) REVERT: r 26 LEU cc_start: 0.9014 (mp) cc_final: 0.8570 (tp) REVERT: t 17 LYS cc_start: 0.9492 (mptt) cc_final: 0.9102 (mmtt) REVERT: t 20 GLU cc_start: 0.9060 (pp20) cc_final: 0.8832 (pp20) REVERT: t 26 LEU cc_start: 0.9029 (mp) cc_final: 0.8576 (tp) outliers start: 14 outliers final: 0 residues processed: 564 average time/residue: 0.2264 time to fit residues: 170.4971 Evaluate side-chains 293 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 0.0870 chunk 62 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.043973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038691 restraints weight = 55714.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040011 restraints weight = 27785.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.040902 restraints weight = 16774.839| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.5662 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= 0.170 Angle : 0.597 4.481 12320 Z= 0.340 Chirality : 0.038 0.128 1460 Planarity : 0.003 0.029 1600 Dihedral : 5.466 34.852 1280 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 1.46 % Allowed : 3.78 % Favored : 94.76 % 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: -3.03 (0.22), residues: 1080 helix: -1.72 (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 G 22 TYR 0.008 0.001 TYR m 8 ARG 0.004 0.000 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 573 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 561 time to evaluate : 1.032 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 TARDY: cannot create tardy model for: "GLN c 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 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: B 1 GLN cc_start: 0.7868 (tp40) cc_final: 0.7473 (tp40) REVERT: D 13 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9061 (mt-10) REVERT: E 1 GLN cc_start: 0.7392 (tp40) cc_final: 0.6979 (tp-100) REVERT: H 1 GLN cc_start: 0.7319 (tp40) cc_final: 0.6771 (tp-100) REVERT: H 5 LEU cc_start: 0.9557 (mt) cc_final: 0.9349 (mt) REVERT: I 1 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6906 (tp-100) REVERT: L 1 GLN cc_start: 0.7164 (tp40) cc_final: 0.6861 (tp40) REVERT: M 13 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8862 (tm-30) REVERT: M 17 LYS cc_start: 0.9526 (mptt) cc_final: 0.8980 (mmmm) REVERT: O 13 GLU cc_start: 0.8910 (mp0) cc_final: 0.8649 (mp0) REVERT: O 17 LYS cc_start: 0.9504 (mptt) cc_final: 0.9071 (mmtt) REVERT: P 20 GLU cc_start: 0.9085 (pp20) cc_final: 0.8877 (pp20) REVERT: Q 1 GLN cc_start: 0.7396 (tp40) cc_final: 0.7024 (tp-100) REVERT: Q 3 GLU cc_start: 0.9075 (pm20) cc_final: 0.8868 (tp30) REVERT: Q 5 LEU cc_start: 0.9658 (mt) cc_final: 0.9314 (mt) REVERT: Q 17 LYS cc_start: 0.9405 (mptt) cc_final: 0.9083 (mmtt) REVERT: Q 18 ILE cc_start: 0.9274 (mt) cc_final: 0.9057 (mt) REVERT: S 4 ILE cc_start: 0.9482 (mt) cc_final: 0.9267 (tt) REVERT: S 13 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8928 (mp0) REVERT: S 17 LYS cc_start: 0.9514 (mptt) cc_final: 0.9224 (mmtt) REVERT: T 5 LEU cc_start: 0.9544 (mt) cc_final: 0.9228 (mt) REVERT: a 1 GLN cc_start: 0.7905 (tp40) cc_final: 0.7630 (tp40) REVERT: a 3 GLU cc_start: 0.9168 (pm20) cc_final: 0.8913 (pm20) REVERT: a 17 LYS cc_start: 0.9515 (mptt) cc_final: 0.9266 (mmtp) REVERT: d 17 LYS cc_start: 0.9424 (mptt) cc_final: 0.9187 (mmtt) REVERT: f 3 GLU cc_start: 0.8954 (tt0) cc_final: 0.8702 (tp30) REVERT: g 13 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8791 (mt-10) REVERT: h 5 LEU cc_start: 0.9609 (mt) cc_final: 0.9364 (mt) REVERT: h 17 LYS cc_start: 0.9410 (mptt) cc_final: 0.8967 (mmtt) REVERT: i 13 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8861 (tm-30) REVERT: i 17 LYS cc_start: 0.9468 (mptt) cc_final: 0.9100 (mmmm) REVERT: i 20 GLU cc_start: 0.8936 (pm20) cc_final: 0.8689 (pm20) REVERT: k 4 ILE cc_start: 0.9412 (mt) cc_final: 0.9207 (tt) REVERT: k 13 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8849 (tm-30) REVERT: k 17 LYS cc_start: 0.9498 (mptt) cc_final: 0.9184 (mmmm) REVERT: k 20 GLU cc_start: 0.8938 (pm20) cc_final: 0.8678 (pm20) REVERT: l 17 LYS cc_start: 0.9490 (mptt) cc_final: 0.9192 (mmtp) REVERT: n 17 LYS cc_start: 0.9437 (mptt) cc_final: 0.8955 (mmtm) REVERT: o 11 ILE cc_start: 0.9363 (mt) cc_final: 0.9050 (pt) REVERT: q 1 GLN cc_start: 0.6877 (tp40) cc_final: 0.6463 (tp40) REVERT: q 3 GLU cc_start: 0.9136 (pm20) cc_final: 0.8922 (pm20) REVERT: q 13 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8637 (mp0) REVERT: q 17 LYS cc_start: 0.9512 (mptt) cc_final: 0.9128 (mmtp) REVERT: q 18 ILE cc_start: 0.9246 (mp) cc_final: 0.9018 (mp) REVERT: r 4 ILE cc_start: 0.9598 (mt) cc_final: 0.9069 (mt) REVERT: r 17 LYS cc_start: 0.9498 (mptt) cc_final: 0.9123 (mmtt) REVERT: r 20 GLU cc_start: 0.9068 (pp20) cc_final: 0.8841 (pp20) REVERT: r 24 GLU cc_start: 0.9173 (tp30) cc_final: 0.8898 (tm-30) REVERT: r 26 LEU cc_start: 0.8955 (mp) cc_final: 0.8556 (tp) REVERT: s 17 LYS cc_start: 0.9440 (mptt) cc_final: 0.9217 (mmtp) REVERT: s 18 ILE cc_start: 0.9191 (mp) cc_final: 0.8951 (mp) REVERT: t 1 GLN cc_start: 0.8440 (mt0) cc_final: 0.8051 (tp-100) REVERT: t 5 LEU cc_start: 0.9465 (mt) cc_final: 0.9167 (mt) REVERT: t 17 LYS cc_start: 0.9489 (mptt) cc_final: 0.9093 (mmtt) REVERT: t 20 GLU cc_start: 0.8993 (pp20) cc_final: 0.8769 (pp20) REVERT: t 26 LEU cc_start: 0.8957 (mp) cc_final: 0.8553 (tp) outliers start: 12 outliers final: 0 residues processed: 561 average time/residue: 0.2256 time to fit residues: 168.9154 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 : 1.112 ------------------------------------------------------------------------------- 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: 0.6980 chunk 65 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** k 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.045519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.039872 restraints weight = 55114.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041256 restraints weight = 28037.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.042196 restraints weight = 17164.831| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9180 Z= 0.175 Angle : 0.613 5.055 12320 Z= 0.350 Chirality : 0.038 0.128 1460 Planarity : 0.002 0.024 1600 Dihedral : 5.331 29.739 1280 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.73 % Allowed : 2.93 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.48 (0.23), residues: 1080 helix: -1.39 (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 G 22 TYR 0.006 0.001 TYR I 8 ARG 0.003 0.000 ARG c 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 560 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 554 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "GLN c 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 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: D 13 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9042 (mt-10) REVERT: A 1 GLN cc_start: 0.7628 (tp40) cc_final: 0.7194 (tp40) REVERT: A 15 ASP cc_start: 0.9556 (m-30) cc_final: 0.9344 (m-30) REVERT: E 1 GLN cc_start: 0.7453 (tp40) cc_final: 0.7079 (tp-100) REVERT: E 15 ASP cc_start: 0.9488 (m-30) cc_final: 0.9283 (m-30) REVERT: E 17 LYS cc_start: 0.9430 (mppt) cc_final: 0.8950 (mmtp) REVERT: H 1 GLN cc_start: 0.7290 (tp40) cc_final: 0.6835 (tp-100) REVERT: H 20 GLU cc_start: 0.9050 (pp20) cc_final: 0.8835 (pp20) REVERT: L 1 GLN cc_start: 0.7414 (tp40) cc_final: 0.7130 (tp40) REVERT: M 13 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8825 (tm-30) REVERT: M 17 LYS cc_start: 0.9399 (mptt) cc_final: 0.8998 (mmmm) REVERT: O 17 LYS cc_start: 0.9517 (mptt) cc_final: 0.9045 (mmtm) REVERT: P 17 LYS cc_start: 0.9451 (mptt) cc_final: 0.8916 (mmtt) REVERT: P 20 GLU cc_start: 0.9008 (pp20) cc_final: 0.8790 (pp20) REVERT: Q 5 LEU cc_start: 0.9627 (mt) cc_final: 0.9228 (mt) REVERT: S 17 LYS cc_start: 0.9500 (mptt) cc_final: 0.9120 (mmtt) REVERT: T 5 LEU cc_start: 0.9565 (mt) cc_final: 0.9332 (mp) REVERT: a 1 GLN cc_start: 0.8236 (tp40) cc_final: 0.8002 (tp40) REVERT: a 3 GLU cc_start: 0.9178 (pm20) cc_final: 0.8919 (pm20) REVERT: a 17 LYS cc_start: 0.9528 (mptt) cc_final: 0.9299 (mmtt) REVERT: a 20 GLU cc_start: 0.9162 (pm20) cc_final: 0.8952 (pm20) REVERT: b 13 GLU cc_start: 0.9039 (mp0) cc_final: 0.8744 (mp0) REVERT: b 17 LYS cc_start: 0.9462 (mptt) cc_final: 0.9109 (mmtt) REVERT: c 13 GLU cc_start: 0.9102 (mp0) cc_final: 0.8805 (mp0) REVERT: c 17 LYS cc_start: 0.9504 (mptt) cc_final: 0.9300 (mmtt) REVERT: f 3 GLU cc_start: 0.8890 (tt0) cc_final: 0.8688 (tp30) REVERT: f 13 GLU cc_start: 0.8937 (mp0) cc_final: 0.8594 (mp0) REVERT: f 17 LYS cc_start: 0.9533 (mptt) cc_final: 0.9241 (mmtt) REVERT: h 5 LEU cc_start: 0.9619 (mt) cc_final: 0.9319 (mt) REVERT: h 17 LYS cc_start: 0.9408 (mptt) cc_final: 0.9032 (mmtt) REVERT: i 1 GLN cc_start: 0.7099 (tp40) cc_final: 0.6716 (tp-100) REVERT: i 5 LEU cc_start: 0.9614 (mt) cc_final: 0.9330 (mp) REVERT: i 13 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8829 (tm-30) REVERT: j 17 LYS cc_start: 0.9443 (mptt) cc_final: 0.9040 (mmtp) REVERT: k 13 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8765 (tm-30) REVERT: k 17 LYS cc_start: 0.9472 (mptt) cc_final: 0.8978 (mmmm) REVERT: l 1 GLN cc_start: 0.7229 (tp40) cc_final: 0.6855 (tp-100) REVERT: n 17 LYS cc_start: 0.9411 (mptt) cc_final: 0.8925 (mmtm) REVERT: n 20 GLU cc_start: 0.8778 (pp20) cc_final: 0.8537 (pp20) REVERT: o 17 LYS cc_start: 0.9477 (mptt) cc_final: 0.8999 (mmmm) REVERT: p 17 LYS cc_start: 0.9443 (mptt) cc_final: 0.8956 (mmtm) REVERT: p 20 GLU cc_start: 0.9034 (pp20) cc_final: 0.8805 (pp20) REVERT: q 3 GLU cc_start: 0.9151 (pm20) cc_final: 0.8934 (pm20) REVERT: r 4 ILE cc_start: 0.9511 (mt) cc_final: 0.9187 (mt) REVERT: r 17 LYS cc_start: 0.9487 (mptt) cc_final: 0.9136 (mmtt) REVERT: r 20 GLU cc_start: 0.9080 (pp20) cc_final: 0.8862 (pp20) REVERT: r 24 GLU cc_start: 0.9205 (tp30) cc_final: 0.8958 (tm-30) REVERT: r 26 LEU cc_start: 0.8978 (mp) cc_final: 0.8607 (tp) REVERT: t 1 GLN cc_start: 0.8473 (mt0) cc_final: 0.8017 (tp-100) REVERT: t 5 LEU cc_start: 0.9413 (mt) cc_final: 0.9201 (mt) REVERT: t 13 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8730 (mp0) REVERT: t 17 LYS cc_start: 0.9456 (mptt) cc_final: 0.9121 (mmtt) REVERT: t 20 GLU cc_start: 0.8997 (pp20) cc_final: 0.8779 (pp20) REVERT: t 26 LEU cc_start: 0.8983 (mp) cc_final: 0.8602 (tp) outliers start: 6 outliers final: 1 residues processed: 554 average time/residue: 0.2281 time to fit residues: 168.4108 Evaluate side-chains 314 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** k 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039720 restraints weight = 55453.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041067 restraints weight = 28659.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.041995 restraints weight = 17670.046| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.6381 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= 0.191 Angle : 0.667 5.474 12320 Z= 0.380 Chirality : 0.040 0.152 1460 Planarity : 0.002 0.014 1600 Dihedral : 5.227 31.737 1280 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -2.23 (0.23), residues: 1080 helix: -1.23 (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 G 22 TYR 0.007 0.001 TYR c 8 ARG 0.002 0.000 ARG c 6 *********************** 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 545 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 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: A 15 ASP cc_start: 0.9535 (m-30) cc_final: 0.9307 (m-30) REVERT: E 1 GLN cc_start: 0.7468 (tp40) cc_final: 0.7189 (tp-100) REVERT: E 17 LYS cc_start: 0.9459 (mptt) cc_final: 0.9046 (mmtt) REVERT: H 1 GLN cc_start: 0.7270 (tp40) cc_final: 0.6825 (tp-100) REVERT: L 1 GLN cc_start: 0.7344 (tp40) cc_final: 0.7073 (tp40) REVERT: M 13 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8822 (tm-30) REVERT: M 17 LYS cc_start: 0.9395 (mptt) cc_final: 0.9026 (mmmm) REVERT: O 13 GLU cc_start: 0.9009 (mp0) cc_final: 0.8629 (mp0) REVERT: O 17 LYS cc_start: 0.9564 (mptt) cc_final: 0.9249 (mmtt) REVERT: P 17 LYS cc_start: 0.9453 (mptt) cc_final: 0.8900 (mmtm) REVERT: P 20 GLU cc_start: 0.9074 (pp20) cc_final: 0.8841 (pp20) REVERT: Q 18 ILE cc_start: 0.9296 (mt) cc_final: 0.9094 (mt) REVERT: S 17 LYS cc_start: 0.9424 (mptt) cc_final: 0.9197 (mmtt) REVERT: T 5 LEU cc_start: 0.9544 (mt) cc_final: 0.9303 (mp) REVERT: a 1 GLN cc_start: 0.8468 (tp40) cc_final: 0.8152 (tp40) REVERT: a 13 GLU cc_start: 0.9111 (pm20) cc_final: 0.8832 (mp0) REVERT: a 17 LYS cc_start: 0.9521 (mptt) cc_final: 0.9209 (mmtt) REVERT: e 13 GLU cc_start: 0.9249 (pm20) cc_final: 0.8881 (mp0) REVERT: e 17 LYS cc_start: 0.9400 (mptt) cc_final: 0.9023 (mmtp) REVERT: f 17 LYS cc_start: 0.9647 (mptt) cc_final: 0.9202 (mmtp) REVERT: f 18 ILE cc_start: 0.9308 (mt) cc_final: 0.9084 (mt) REVERT: g 13 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8904 (mt-10) REVERT: h 5 LEU cc_start: 0.9628 (mt) cc_final: 0.9425 (mt) REVERT: h 17 LYS cc_start: 0.9408 (mptt) cc_final: 0.9041 (mmtt) REVERT: i 1 GLN cc_start: 0.7192 (tp40) cc_final: 0.6791 (tp-100) REVERT: i 5 LEU cc_start: 0.9624 (mt) cc_final: 0.9322 (mp) REVERT: j 17 LYS cc_start: 0.9463 (mptt) cc_final: 0.9073 (mmtp) REVERT: l 1 GLN cc_start: 0.7164 (tp40) cc_final: 0.6796 (tp-100) REVERT: n 17 LYS cc_start: 0.9432 (mptt) cc_final: 0.8956 (mmtm) REVERT: n 20 GLU cc_start: 0.8763 (pp20) cc_final: 0.8500 (pp20) REVERT: o 17 LYS cc_start: 0.9474 (mptt) cc_final: 0.9102 (mmtm) REVERT: p 17 LYS cc_start: 0.9471 (mptt) cc_final: 0.9095 (mmtt) REVERT: p 20 GLU cc_start: 0.8999 (pp20) cc_final: 0.8786 (pp20) REVERT: r 4 ILE cc_start: 0.9505 (mt) cc_final: 0.9199 (mt) REVERT: r 17 LYS cc_start: 0.9482 (mptt) cc_final: 0.9129 (mmtt) REVERT: r 20 GLU cc_start: 0.9096 (pp20) cc_final: 0.8852 (pp20) REVERT: r 24 GLU cc_start: 0.9215 (tp30) cc_final: 0.8984 (tm-30) REVERT: r 26 LEU cc_start: 0.9000 (mp) cc_final: 0.8618 (tp) REVERT: t 1 GLN cc_start: 0.8437 (mt0) cc_final: 0.8114 (tp-100) REVERT: t 17 LYS cc_start: 0.9448 (mptt) cc_final: 0.9100 (mmtt) REVERT: t 20 GLU cc_start: 0.9006 (pp20) cc_final: 0.8778 (pp20) REVERT: t 26 LEU cc_start: 0.8976 (mp) cc_final: 0.8592 (tp) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.2305 time to fit residues: 168.2750 Evaluate side-chains 336 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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: 0.0060 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 29 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 overall best weight: 0.5414 ------------------------------------------------------------------------------- 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** R 1 GLN S 29 GLN k 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.039853 restraints weight = 54517.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.041268 restraints weight = 28940.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042224 restraints weight = 18044.631| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9180 Z= 0.195 Angle : 0.715 5.611 12320 Z= 0.400 Chirality : 0.041 0.148 1460 Planarity : 0.002 0.013 1600 Dihedral : 5.191 32.972 1280 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -2.01 (0.23), residues: 1080 helix: -1.09 (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 G 22 TYR 0.007 0.001 TYR J 8 ARG 0.004 0.000 ARG n 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 552 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN S 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 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: B 15 ASP cc_start: 0.9462 (m-30) cc_final: 0.9206 (m-30) REVERT: D 13 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8517 (mt-10) REVERT: D 17 LYS cc_start: 0.9563 (mptt) cc_final: 0.9119 (mmtp) REVERT: A 15 ASP cc_start: 0.9493 (m-30) cc_final: 0.9237 (m-30) REVERT: E 1 GLN cc_start: 0.7367 (tp40) cc_final: 0.6951 (tp40) REVERT: F 17 LYS cc_start: 0.9471 (mptt) cc_final: 0.9076 (mmtt) REVERT: G 17 LYS cc_start: 0.9511 (mptt) cc_final: 0.9171 (mmtp) REVERT: H 1 GLN cc_start: 0.7282 (tp40) cc_final: 0.6839 (tp40) REVERT: H 5 LEU cc_start: 0.9558 (mt) cc_final: 0.9348 (mt) REVERT: H 20 GLU cc_start: 0.9000 (pp20) cc_final: 0.8782 (pp20) REVERT: J 13 GLU cc_start: 0.9018 (pm20) cc_final: 0.8776 (mp0) REVERT: J 17 LYS cc_start: 0.9448 (mptt) cc_final: 0.9008 (mmtp) REVERT: L 1 GLN cc_start: 0.7423 (tp40) cc_final: 0.7166 (tp40) REVERT: L 15 ASP cc_start: 0.9524 (m-30) cc_final: 0.9187 (m-30) REVERT: M 13 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8820 (tm-30) REVERT: M 17 LYS cc_start: 0.9369 (mptt) cc_final: 0.8987 (mmmm) REVERT: N 15 ASP cc_start: 0.9266 (m-30) cc_final: 0.9059 (m-30) REVERT: O 17 LYS cc_start: 0.9559 (mptt) cc_final: 0.9181 (mmtt) REVERT: P 17 LYS cc_start: 0.9456 (mptt) cc_final: 0.8939 (mmtm) REVERT: P 20 GLU cc_start: 0.9059 (pp20) cc_final: 0.8823 (pp20) REVERT: Q 1 GLN cc_start: 0.7412 (tp40) cc_final: 0.7034 (tp40) REVERT: Q 5 LEU cc_start: 0.9641 (mt) cc_final: 0.9385 (mp) REVERT: Q 13 GLU cc_start: 0.8993 (pm20) cc_final: 0.8697 (mp0) REVERT: Q 17 LYS cc_start: 0.9386 (mptt) cc_final: 0.9080 (mmtp) REVERT: Q 18 ILE cc_start: 0.9284 (mt) cc_final: 0.9065 (mt) REVERT: R 17 LYS cc_start: 0.9422 (mmtt) cc_final: 0.9001 (mmtm) REVERT: S 17 LYS cc_start: 0.9504 (mptt) cc_final: 0.9095 (mmtt) REVERT: a 1 GLN cc_start: 0.8506 (tp40) cc_final: 0.8292 (tp40) REVERT: a 20 GLU cc_start: 0.9141 (pm20) cc_final: 0.8928 (pm20) REVERT: b 13 GLU cc_start: 0.9097 (mp0) cc_final: 0.8769 (mp0) REVERT: b 17 LYS cc_start: 0.9420 (mptt) cc_final: 0.9134 (mmtt) REVERT: f 13 GLU cc_start: 0.9027 (mp0) cc_final: 0.8713 (mp0) REVERT: f 17 LYS cc_start: 0.9577 (mptt) cc_final: 0.9281 (mmtp) REVERT: g 13 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8839 (mt-10) REVERT: g 27 LYS cc_start: 0.9122 (tptp) cc_final: 0.8841 (ttmt) REVERT: h 5 LEU cc_start: 0.9632 (mt) cc_final: 0.9402 (mt) REVERT: h 12 LEU cc_start: 0.9418 (mm) cc_final: 0.9062 (tp) REVERT: h 17 LYS cc_start: 0.9377 (mptt) cc_final: 0.9105 (mmtp) REVERT: i 1 GLN cc_start: 0.7232 (tp40) cc_final: 0.6852 (tp-100) REVERT: i 5 LEU cc_start: 0.9576 (mt) cc_final: 0.9331 (mp) REVERT: l 1 GLN cc_start: 0.7134 (tp40) cc_final: 0.6798 (tp-100) REVERT: m 15 ASP cc_start: 0.8902 (m-30) cc_final: 0.8631 (t0) REVERT: n 12 LEU cc_start: 0.9544 (mm) cc_final: 0.9199 (tp) REVERT: n 17 LYS cc_start: 0.9413 (mptt) cc_final: 0.8978 (mmtm) REVERT: p 20 GLU cc_start: 0.9057 (pp20) cc_final: 0.8820 (pp20) REVERT: q 3 GLU cc_start: 0.9369 (pm20) cc_final: 0.8966 (pm20) REVERT: r 15 ASP cc_start: 0.9451 (m-30) cc_final: 0.9209 (m-30) REVERT: r 17 LYS cc_start: 0.9471 (mptt) cc_final: 0.9113 (mmtt) REVERT: r 18 ILE cc_start: 0.9127 (mt) cc_final: 0.8917 (mt) REVERT: r 20 GLU cc_start: 0.9015 (pp20) cc_final: 0.8814 (pp20) REVERT: r 26 LEU cc_start: 0.8943 (mp) cc_final: 0.8584 (tp) REVERT: s 17 LYS cc_start: 0.9444 (mptt) cc_final: 0.9178 (mmtp) REVERT: t 1 GLN cc_start: 0.8596 (mt0) cc_final: 0.8165 (tm-30) REVERT: t 17 LYS cc_start: 0.9446 (mptt) cc_final: 0.9124 (mmtt) REVERT: t 26 LEU cc_start: 0.8928 (mp) cc_final: 0.8550 (tp) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 0.2210 time to fit residues: 162.9451 Evaluate side-chains 346 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** k 1 GLN ** n 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.045403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.039501 restraints weight = 55648.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.040927 restraints weight = 29409.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.041874 restraints weight = 18223.800| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.6931 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= 0.224 Angle : 0.808 6.282 12320 Z= 0.457 Chirality : 0.044 0.170 1460 Planarity : 0.002 0.015 1600 Dihedral : 5.068 30.046 1280 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -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 0.001 0.000 HIS G 22 TYR 0.008 0.001 TYR Q 8 ARG 0.002 0.000 ARG n 10 *********************** 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 541 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN J 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN R 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN S 1 " (corrupted residue). Skipping it. 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 f 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 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: E 17 LYS cc_start: 0.9422 (mptt) cc_final: 0.9152 (mmtp) REVERT: F 17 LYS cc_start: 0.9540 (mptt) cc_final: 0.9276 (mmtt) REVERT: H 1 GLN cc_start: 0.7391 (tp40) cc_final: 0.7161 (tp40) REVERT: H 20 GLU cc_start: 0.8987 (pp20) cc_final: 0.8754 (pp20) REVERT: I 1 GLN cc_start: 0.8069 (tp40) cc_final: 0.7792 (tp40) REVERT: J 13 GLU cc_start: 0.9011 (pm20) cc_final: 0.8744 (mp0) REVERT: J 17 LYS cc_start: 0.9379 (mptt) cc_final: 0.9070 (mmtp) REVERT: L 1 GLN cc_start: 0.7439 (tp40) cc_final: 0.7167 (tp40) REVERT: L 13 GLU cc_start: 0.9145 (pm20) cc_final: 0.8860 (mp0) REVERT: L 15 ASP cc_start: 0.9549 (m-30) cc_final: 0.9224 (m-30) REVERT: L 17 LYS cc_start: 0.9436 (mptt) cc_final: 0.8898 (mmtp) REVERT: M 13 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8917 (tm-30) REVERT: M 15 ASP cc_start: 0.9425 (m-30) cc_final: 0.9221 (m-30) REVERT: M 17 LYS cc_start: 0.9404 (mptt) cc_final: 0.8943 (mmmt) REVERT: N 13 GLU cc_start: 0.9162 (pm20) cc_final: 0.8953 (mp0) REVERT: N 15 ASP cc_start: 0.9356 (m-30) cc_final: 0.9147 (m-30) REVERT: N 17 LYS cc_start: 0.9404 (mptt) cc_final: 0.8982 (mmtp) REVERT: O 13 GLU cc_start: 0.9084 (mp0) cc_final: 0.8658 (mp0) REVERT: O 17 LYS cc_start: 0.9594 (mptt) cc_final: 0.9183 (mmtt) REVERT: P 17 LYS cc_start: 0.9448 (mptt) cc_final: 0.8859 (mmtm) REVERT: P 20 GLU cc_start: 0.9042 (pp20) cc_final: 0.8796 (pp20) REVERT: Q 1 GLN cc_start: 0.7473 (tp40) cc_final: 0.7043 (tp40) REVERT: Q 5 LEU cc_start: 0.9634 (mt) cc_final: 0.9378 (mp) REVERT: R 17 LYS cc_start: 0.9652 (mmtt) cc_final: 0.9310 (mmtm) REVERT: T 17 LYS cc_start: 0.9532 (mmtt) cc_final: 0.9172 (mmtm) REVERT: a 1 GLN cc_start: 0.8644 (tp40) cc_final: 0.8384 (tp40) REVERT: a 3 GLU cc_start: 0.9235 (pm20) cc_final: 0.8938 (pm20) REVERT: a 20 GLU cc_start: 0.9137 (pm20) cc_final: 0.8692 (pm20) REVERT: c 13 GLU cc_start: 0.9038 (pm20) cc_final: 0.8693 (mp0) REVERT: c 17 LYS cc_start: 0.9407 (mptt) cc_final: 0.9019 (mmtp) REVERT: d 17 LYS cc_start: 0.9466 (mptt) cc_final: 0.9136 (mmmm) REVERT: e 13 GLU cc_start: 0.9268 (pm20) cc_final: 0.8815 (mp0) REVERT: e 17 LYS cc_start: 0.9355 (mptt) cc_final: 0.9027 (mmtp) REVERT: f 13 GLU cc_start: 0.9002 (mp0) cc_final: 0.8746 (mp0) REVERT: f 17 LYS cc_start: 0.9594 (mptt) cc_final: 0.9218 (mmtp) REVERT: g 13 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8752 (mt-10) REVERT: g 18 ILE cc_start: 0.9078 (mt) cc_final: 0.8869 (mt) REVERT: h 12 LEU cc_start: 0.9433 (mm) cc_final: 0.9086 (tp) REVERT: h 17 LYS cc_start: 0.9378 (mptt) cc_final: 0.9120 (mmtp) REVERT: i 1 GLN cc_start: 0.7285 (tp40) cc_final: 0.6895 (tp-100) REVERT: i 5 LEU cc_start: 0.9566 (mt) cc_final: 0.9338 (mp) REVERT: j 19 LEU cc_start: 0.9239 (mm) cc_final: 0.9036 (mm) REVERT: l 1 GLN cc_start: 0.7175 (tp40) cc_final: 0.6826 (tp-100) REVERT: l 17 LYS cc_start: 0.9545 (mptt) cc_final: 0.9271 (mmtp) REVERT: m 15 ASP cc_start: 0.8945 (m-30) cc_final: 0.8673 (t0) REVERT: n 17 LYS cc_start: 0.9487 (mptt) cc_final: 0.9158 (mmtt) REVERT: p 12 LEU cc_start: 0.9531 (mm) cc_final: 0.9064 (tp) REVERT: p 17 LYS cc_start: 0.9472 (mptt) cc_final: 0.8974 (mmtm) REVERT: p 20 GLU cc_start: 0.9047 (pp20) cc_final: 0.8845 (pp20) REVERT: r 17 LYS cc_start: 0.9431 (mptt) cc_final: 0.9106 (mmtt) REVERT: r 20 GLU cc_start: 0.9087 (pp20) cc_final: 0.8833 (pp20) REVERT: r 26 LEU cc_start: 0.8985 (mp) cc_final: 0.8635 (tp) REVERT: s 17 LYS cc_start: 0.9445 (mptt) cc_final: 0.9157 (mmtp) REVERT: t 1 GLN cc_start: 0.8611 (mt0) cc_final: 0.8301 (tm-30) REVERT: t 17 LYS cc_start: 0.9444 (mptt) cc_final: 0.9139 (mmtp) REVERT: t 18 ILE cc_start: 0.9139 (mt) cc_final: 0.8845 (mt) REVERT: t 20 GLU cc_start: 0.8907 (pp20) cc_final: 0.8656 (pp20) REVERT: t 26 LEU cc_start: 0.8962 (mp) cc_final: 0.8604 (tp) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.2241 time to fit residues: 161.8967 Evaluate side-chains 356 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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: 2.9990 chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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** k 1 GLN ** n 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 = 0.3136 r_free = 0.3136 target = 0.043710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.038298 restraints weight = 57255.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039658 restraints weight = 29800.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040577 restraints weight = 18319.628| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9180 Z= 0.267 Angle : 0.850 6.336 12320 Z= 0.484 Chirality : 0.045 0.192 1460 Planarity : 0.003 0.025 1600 Dihedral : 5.322 33.293 1280 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.03 (0.22), residues: 1080 helix: -1.11 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 22 TYR 0.006 0.001 TYR e 8 ARG 0.003 0.000 ARG A 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 526 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "GLN f 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: A 17 LYS cc_start: 0.9626 (mptt) cc_final: 0.9200 (mmtm) REVERT: E 17 LYS cc_start: 0.9427 (mptt) cc_final: 0.9088 (mmtp) REVERT: E 29 GLN cc_start: 0.8822 (tt0) cc_final: 0.8614 (tt0) REVERT: G 24 GLU cc_start: 0.9173 (tp30) cc_final: 0.8815 (tm-30) REVERT: H 1 GLN cc_start: 0.7338 (tp40) cc_final: 0.6841 (tp40) REVERT: H 5 LEU cc_start: 0.9537 (mt) cc_final: 0.9333 (mt) REVERT: I 1 GLN cc_start: 0.8509 (tp40) cc_final: 0.8306 (tp40) REVERT: J 17 LYS cc_start: 0.9460 (mptt) cc_final: 0.9000 (mmtp) REVERT: L 1 GLN cc_start: 0.7380 (tp40) cc_final: 0.7046 (tp-100) REVERT: L 5 LEU cc_start: 0.9678 (mt) cc_final: 0.9464 (mt) REVERT: L 15 ASP cc_start: 0.9533 (m-30) cc_final: 0.9230 (m-30) REVERT: N 15 ASP cc_start: 0.9446 (m-30) cc_final: 0.9215 (m-30) REVERT: N 17 LYS cc_start: 0.9455 (mptt) cc_final: 0.9112 (mmtp) REVERT: P 12 LEU cc_start: 0.9524 (mm) cc_final: 0.9212 (tp) REVERT: P 20 GLU cc_start: 0.9055 (pp20) cc_final: 0.8790 (pp20) REVERT: Q 1 GLN cc_start: 0.7502 (tp40) cc_final: 0.7158 (tm-30) REVERT: Q 5 LEU cc_start: 0.9653 (mt) cc_final: 0.9395 (mt) REVERT: Q 18 ILE cc_start: 0.9379 (mt) cc_final: 0.9166 (mt) REVERT: S 12 LEU cc_start: 0.9540 (mm) cc_final: 0.9286 (tp) REVERT: S 27 LYS cc_start: 0.8962 (tmtt) cc_final: 0.8681 (ttmm) REVERT: T 1 GLN cc_start: 0.8517 (tp40) cc_final: 0.8290 (tp40) REVERT: T 29 GLN cc_start: 0.8674 (mt0) cc_final: 0.8445 (mt0) REVERT: a 1 GLN cc_start: 0.8820 (tp40) cc_final: 0.8547 (tp40) REVERT: a 20 GLU cc_start: 0.9161 (pm20) cc_final: 0.8944 (pm20) REVERT: b 13 GLU cc_start: 0.9180 (mp0) cc_final: 0.8745 (mp0) REVERT: b 17 LYS cc_start: 0.9516 (mptt) cc_final: 0.9201 (mmtp) REVERT: b 20 GLU cc_start: 0.9047 (pm20) cc_final: 0.8814 (pm20) REVERT: c 13 GLU cc_start: 0.9055 (pm20) cc_final: 0.8780 (mp0) REVERT: c 17 LYS cc_start: 0.9455 (mptt) cc_final: 0.8983 (mmtp) REVERT: c 18 ILE cc_start: 0.9308 (mt) cc_final: 0.9086 (mt) REVERT: e 13 GLU cc_start: 0.9246 (pm20) cc_final: 0.8848 (mp0) REVERT: e 17 LYS cc_start: 0.9372 (mptt) cc_final: 0.9007 (mmtp) REVERT: f 13 GLU cc_start: 0.9053 (mp0) cc_final: 0.8826 (mp0) REVERT: f 17 LYS cc_start: 0.9619 (mptt) cc_final: 0.9271 (mmtp) REVERT: g 13 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8787 (mt-10) REVERT: h 12 LEU cc_start: 0.9480 (mm) cc_final: 0.9250 (tp) REVERT: h 17 LYS cc_start: 0.9460 (mptt) cc_final: 0.9031 (mmtp) REVERT: i 1 GLN cc_start: 0.7177 (tp40) cc_final: 0.6782 (tp-100) REVERT: i 5 LEU cc_start: 0.9626 (mt) cc_final: 0.9251 (mp) REVERT: l 1 GLN cc_start: 0.7213 (tp40) cc_final: 0.6847 (tp-100) REVERT: l 15 ASP cc_start: 0.9180 (m-30) cc_final: 0.8953 (m-30) REVERT: l 17 LYS cc_start: 0.9554 (mptt) cc_final: 0.9247 (mmtp) REVERT: m 15 ASP cc_start: 0.8990 (m-30) cc_final: 0.8694 (t0) REVERT: m 17 LYS cc_start: 0.9558 (mptt) cc_final: 0.9166 (mmtt) REVERT: n 17 LYS cc_start: 0.9540 (mptt) cc_final: 0.9242 (mmtm) REVERT: o 17 LYS cc_start: 0.9461 (mptt) cc_final: 0.8997 (mmmm) REVERT: p 12 LEU cc_start: 0.9559 (mm) cc_final: 0.9210 (tp) REVERT: p 17 LYS cc_start: 0.9481 (mptt) cc_final: 0.8941 (mmtm) REVERT: r 20 GLU cc_start: 0.9176 (pp20) cc_final: 0.8938 (pp20) REVERT: r 26 LEU cc_start: 0.8980 (mp) cc_final: 0.8638 (tp) REVERT: s 17 LYS cc_start: 0.9536 (mptt) cc_final: 0.9305 (mmtp) REVERT: t 1 GLN cc_start: 0.8590 (mt0) cc_final: 0.8271 (tp-100) REVERT: t 15 ASP cc_start: 0.9416 (m-30) cc_final: 0.9161 (m-30) REVERT: t 17 LYS cc_start: 0.9454 (mptt) cc_final: 0.9140 (mmtp) REVERT: t 18 ILE cc_start: 0.9182 (mt) cc_final: 0.8958 (mt) REVERT: t 20 GLU cc_start: 0.9013 (pp20) cc_final: 0.8755 (pp20) REVERT: t 26 LEU cc_start: 0.9115 (mp) cc_final: 0.8692 (tp) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.2317 time to fit residues: 162.2965 Evaluate side-chains 361 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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: 0.5980 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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** k 1 GLN ** n 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 = 0.3187 r_free = 0.3187 target = 0.045575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039869 restraints weight = 55160.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041318 restraints weight = 28867.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.042299 restraints weight = 17683.433| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9180 Z= 0.253 Angle : 0.914 6.688 12320 Z= 0.512 Chirality : 0.045 0.180 1460 Planarity : 0.003 0.016 1600 Dihedral : 5.375 38.181 1280 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.95 (0.23), residues: 1080 helix: -1.06 (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 I 22 TYR 0.008 0.001 TYR Q 8 ARG 0.006 0.000 ARG h 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 538 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "GLN R 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN f 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN o 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7856 (tp40) REVERT: E 17 LYS cc_start: 0.9401 (mptt) cc_final: 0.9074 (mmtp) REVERT: G 17 LYS cc_start: 0.9451 (mptt) cc_final: 0.9163 (mmtp) REVERT: H 1 GLN cc_start: 0.7362 (tp40) cc_final: 0.7137 (tp40) REVERT: J 13 GLU cc_start: 0.8881 (pm20) cc_final: 0.8584 (mp0) REVERT: J 17 LYS cc_start: 0.9507 (mptt) cc_final: 0.9104 (mmtp) REVERT: L 1 GLN cc_start: 0.7456 (tp40) cc_final: 0.7173 (tp40) REVERT: L 15 ASP cc_start: 0.9521 (m-30) cc_final: 0.9202 (m-30) REVERT: N 15 ASP cc_start: 0.9425 (m-30) cc_final: 0.9165 (m-30) REVERT: O 17 LYS cc_start: 0.9576 (mptt) cc_final: 0.9186 (mmtt) REVERT: Q 1 GLN cc_start: 0.7594 (tp40) cc_final: 0.7251 (tp40) REVERT: Q 5 LEU cc_start: 0.9636 (mt) cc_final: 0.9316 (mp) REVERT: R 17 LYS cc_start: 0.9647 (mmtt) cc_final: 0.9340 (mmtm) REVERT: S 12 LEU cc_start: 0.9494 (mm) cc_final: 0.9219 (tp) REVERT: S 27 LYS cc_start: 0.8890 (tmtt) cc_final: 0.8653 (ttmm) REVERT: T 17 LYS cc_start: 0.9431 (mmtt) cc_final: 0.9054 (mmtm) REVERT: b 13 GLU cc_start: 0.9130 (mp0) cc_final: 0.8577 (mp0) REVERT: b 17 LYS cc_start: 0.9477 (mptt) cc_final: 0.9187 (mmtp) REVERT: b 20 GLU cc_start: 0.8907 (pm20) cc_final: 0.8672 (pm20) REVERT: c 15 ASP cc_start: 0.9339 (m-30) cc_final: 0.9104 (m-30) REVERT: c 18 ILE cc_start: 0.9228 (mt) cc_final: 0.8956 (mt) REVERT: d 13 GLU cc_start: 0.9085 (pm20) cc_final: 0.8806 (pm20) REVERT: e 3 GLU cc_start: 0.9091 (pm20) cc_final: 0.8758 (pm20) REVERT: e 13 GLU cc_start: 0.9183 (pm20) cc_final: 0.8781 (mp0) REVERT: e 17 LYS cc_start: 0.9336 (mptt) cc_final: 0.9028 (mmtp) REVERT: f 17 LYS cc_start: 0.9571 (mptt) cc_final: 0.9239 (mmtp) REVERT: g 13 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8736 (mt-10) REVERT: l 1 GLN cc_start: 0.7175 (tp40) cc_final: 0.6822 (tp40) REVERT: m 15 ASP cc_start: 0.8860 (m-30) cc_final: 0.8615 (t0) REVERT: m 17 LYS cc_start: 0.9569 (mptt) cc_final: 0.9356 (mmtt) REVERT: n 17 LYS cc_start: 0.9493 (mptt) cc_final: 0.9185 (mmtt) REVERT: o 17 LYS cc_start: 0.9451 (mptt) cc_final: 0.9040 (mmtm) REVERT: p 12 LEU cc_start: 0.9495 (mm) cc_final: 0.9133 (tp) REVERT: p 17 LYS cc_start: 0.9430 (mptt) cc_final: 0.8954 (mmtm) REVERT: p 20 GLU cc_start: 0.8865 (pp20) cc_final: 0.8661 (pp20) REVERT: r 17 LYS cc_start: 0.9400 (mptt) cc_final: 0.9120 (mmtt) REVERT: r 20 GLU cc_start: 0.9031 (pp20) cc_final: 0.8810 (pp20) REVERT: r 26 LEU cc_start: 0.8944 (mp) cc_final: 0.8572 (tp) REVERT: t 15 ASP cc_start: 0.9365 (m-30) cc_final: 0.9065 (m-30) REVERT: t 17 LYS cc_start: 0.9437 (mptt) cc_final: 0.9164 (mmtt) REVERT: t 18 ILE cc_start: 0.9144 (mt) cc_final: 0.8943 (mt) REVERT: t 20 GLU cc_start: 0.8858 (pp20) cc_final: 0.8631 (pp20) REVERT: t 26 LEU cc_start: 0.8956 (mp) cc_final: 0.8614 (tp) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.2289 time to fit residues: 163.1867 Evaluate side-chains 373 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- 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** k 1 GLN ** n 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 = 0.3147 r_free = 0.3147 target = 0.044370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.038900 restraints weight = 55409.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.040286 restraints weight = 29540.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.041210 restraints weight = 18189.652| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9180 Z= 0.277 Angle : 0.930 7.374 12320 Z= 0.529 Chirality : 0.046 0.189 1460 Planarity : 0.003 0.020 1600 Dihedral : 5.286 37.725 1280 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.85 (0.23), residues: 1080 helix: -1.00 (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 T 22 TYR 0.007 0.001 TYR e 8 ARG 0.002 0.000 ARG q 6 =============================================================================== Job complete usr+sys time: 3413.98 seconds wall clock time: 61 minutes 35.95 seconds (3695.95 seconds total)