Starting phenix.real_space_refine (version: dev) on Sun Feb 19 01:28:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wky_21813/02_2023/6wky_21813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wky_21813/02_2023/6wky_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wky_21813/02_2023/6wky_21813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wky_21813/02_2023/6wky_21813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wky_21813/02_2023/6wky_21813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wky_21813/02_2023/6wky_21813.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.24, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.91 Conformation dependent library (CDL) restraints added in 1.5 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: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 1 through 28 removed outlier: 3.890A pdb=" N TYR B 8 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 28 removed outlier: 3.726A pdb=" N TYR C 8 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 19 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 28 removed outlier: 3.832A pdb=" N TYR D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA D 9 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP D 15 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 19 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 28 removed outlier: 4.255A pdb=" N TYR A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.531A pdb=" N ARG E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR E 8 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 9 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP E 15 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 19 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 21 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU E 24 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 26 " --> pdb=" O HIS E 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 28 removed outlier: 3.961A pdb=" N TYR F 8 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA F 14 " --> pdb=" O ARG F 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 19 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU F 26 " --> pdb=" O HIS F 22 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 21 removed outlier: 3.726A pdb=" N TYR G 8 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP G 15 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 21 " --> pdb=" O LYS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'H' and resid 2 through 28 removed outlier: 3.605A pdb=" N ARG H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA H 14 " --> pdb=" O ARG H 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP H 15 " --> pdb=" O ILE H 11 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU H 26 " --> pdb=" O HIS H 22 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 28 removed outlier: 4.076A pdb=" N TYR I 8 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA I 9 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG I 10 " --> pdb=" O ARG I 6 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 14 " --> pdb=" O ARG I 10 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU I 19 " --> pdb=" O ASP I 15 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA I 21 " --> pdb=" O LYS I 17 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU I 24 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU I 26 " --> pdb=" O HIS I 22 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA I 28 " --> pdb=" O GLU I 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 28 removed outlier: 3.828A pdb=" N TYR J 8 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA J 9 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG J 10 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA J 14 " --> pdb=" O ARG J 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA J 16 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 19 " --> pdb=" O ASP J 15 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU J 26 " --> pdb=" O HIS J 22 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 28 removed outlier: 3.928A pdb=" N TYR K 8 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA K 9 " --> pdb=" O LEU K 5 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA K 14 " --> pdb=" O ARG K 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA K 16 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU K 19 " --> pdb=" O ASP K 15 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA K 21 " --> pdb=" O LYS K 17 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU K 26 " --> pdb=" O HIS K 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 28 removed outlier: 4.136A pdb=" N TYR L 8 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA L 9 " --> pdb=" O LEU L 5 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG L 10 " --> pdb=" O ARG L 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA L 14 " --> pdb=" O ARG L 10 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 19 " --> pdb=" O ASP L 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA L 21 " --> pdb=" O LYS L 17 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU L 26 " --> pdb=" O HIS L 22 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 28 " --> pdb=" O GLU L 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 28 removed outlier: 4.176A pdb=" N TYR M 8 " --> pdb=" O ILE M 4 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA M 9 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG M 10 " --> pdb=" O ARG M 6 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA M 14 " --> pdb=" O ARG M 10 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS M 17 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU M 19 " --> pdb=" O ASP M 15 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA M 21 " --> pdb=" O LYS M 17 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU M 26 " --> pdb=" O HIS M 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 28 removed outlier: 3.719A pdb=" N TYR N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG N 10 " --> pdb=" O ARG N 6 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA N 16 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS N 17 " --> pdb=" O GLU N 13 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU N 19 " --> pdb=" O ASP N 15 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA N 21 " --> pdb=" O LYS N 17 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU N 26 " --> pdb=" O HIS N 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 28 removed outlier: 3.962A pdb=" N TYR O 8 " --> pdb=" O ILE O 4 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA O 9 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG O 10 " --> pdb=" O ARG O 6 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA O 16 " --> pdb=" O LEU O 12 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS O 17 " --> pdb=" O GLU O 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU O 19 " --> pdb=" O ASP O 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU O 26 " --> pdb=" O HIS O 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 removed outlier: 4.251A pdb=" N TYR P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA P 9 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG P 10 " --> pdb=" O ARG P 6 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP P 15 " --> pdb=" O ILE P 11 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS P 17 " --> pdb=" O GLU P 13 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA P 21 " --> pdb=" O LYS P 17 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU P 26 " --> pdb=" O HIS P 22 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA P 28 " --> pdb=" O GLU P 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 28 removed outlier: 3.921A pdb=" N TYR Q 8 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Q 9 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA Q 16 " --> pdb=" O LEU Q 12 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS Q 17 " --> pdb=" O GLU Q 13 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU Q 19 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA Q 21 " --> pdb=" O LYS Q 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU Q 24 " --> pdb=" O GLU Q 20 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU Q 26 " --> pdb=" O HIS Q 22 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA Q 28 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 28 removed outlier: 3.687A pdb=" N TYR R 8 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA R 9 " --> pdb=" O LEU R 5 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG R 10 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA R 14 " --> pdb=" O ARG R 10 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP R 15 " --> pdb=" O ILE R 11 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA R 16 " --> pdb=" O LEU R 12 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS R 17 " --> pdb=" O GLU R 13 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU R 19 " --> pdb=" O ASP R 15 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA R 21 " --> pdb=" O LYS R 17 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU R 26 " --> pdb=" O HIS R 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 28 removed outlier: 3.889A pdb=" N TYR S 8 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA S 9 " --> pdb=" O LEU S 5 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG S 10 " --> pdb=" O ARG S 6 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA S 14 " --> pdb=" O ARG S 10 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP S 15 " --> pdb=" O ILE S 11 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS S 17 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU S 19 " --> pdb=" O ASP S 15 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA S 21 " --> pdb=" O LYS S 17 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU S 24 " --> pdb=" O GLU S 20 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU S 26 " --> pdb=" O HIS S 22 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA S 28 " --> pdb=" O GLU S 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 28 removed outlier: 4.146A pdb=" N TYR T 8 " --> pdb=" O ILE T 4 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA T 9 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA T 14 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP T 15 " --> pdb=" O ILE T 11 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA T 16 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU T 19 " --> pdb=" O ASP T 15 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA T 21 " --> pdb=" O LYS T 17 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU T 26 " --> pdb=" O HIS T 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA T 28 " --> pdb=" O GLU T 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 28 removed outlier: 3.893A pdb=" N TYR a 8 " --> pdb=" O ILE a 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA a 9 " --> pdb=" O LEU a 5 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG a 10 " --> pdb=" O ARG a 6 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA a 14 " --> pdb=" O ARG a 10 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS a 17 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU a 19 " --> pdb=" O ASP a 15 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA a 21 " --> pdb=" O LYS a 17 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU a 26 " --> pdb=" O HIS a 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 28 removed outlier: 3.703A pdb=" N TYR b 8 " --> pdb=" O ILE b 4 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA b 9 " --> pdb=" O LEU b 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG b 10 " --> pdb=" O ARG b 6 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA b 14 " --> pdb=" O ARG b 10 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA b 16 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU b 19 " --> pdb=" O ASP b 15 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA b 21 " --> pdb=" O LYS b 17 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU b 26 " --> pdb=" O HIS b 22 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA b 28 " --> pdb=" O GLU b 24 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 28 removed outlier: 3.947A pdb=" N TYR c 8 " --> pdb=" O ILE c 4 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA c 9 " --> pdb=" O LEU c 5 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG c 10 " --> pdb=" O ARG c 6 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA c 14 " --> pdb=" O ARG c 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA c 16 " --> pdb=" O LEU c 12 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU c 19 " --> pdb=" O ASP c 15 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA c 21 " --> pdb=" O LYS c 17 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU c 24 " --> pdb=" O GLU c 20 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU c 26 " --> pdb=" O HIS c 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 28 removed outlier: 4.090A pdb=" N TYR d 8 " --> pdb=" O ILE d 4 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA d 9 " --> pdb=" O LEU d 5 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG d 10 " --> pdb=" O ARG d 6 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA d 16 " --> pdb=" O LEU d 12 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS d 17 " --> pdb=" O GLU d 13 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU d 19 " --> pdb=" O ASP d 15 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA d 21 " --> pdb=" O LYS d 17 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU d 26 " --> pdb=" O HIS d 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA d 28 " --> pdb=" O GLU d 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 28 removed outlier: 3.755A pdb=" N TYR e 8 " --> pdb=" O ILE e 4 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA e 9 " --> pdb=" O LEU e 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG e 10 " --> pdb=" O ARG e 6 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA e 14 " --> pdb=" O ARG e 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA e 16 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS e 17 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU e 19 " --> pdb=" O ASP e 15 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA e 21 " --> pdb=" O LYS e 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU e 24 " --> pdb=" O GLU e 20 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU e 26 " --> pdb=" O HIS e 22 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA e 28 " --> pdb=" O GLU e 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 28 removed outlier: 3.662A pdb=" N TYR f 8 " --> pdb=" O ILE f 4 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA f 9 " --> pdb=" O LEU f 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG f 10 " --> pdb=" O ARG f 6 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP f 15 " --> pdb=" O ILE f 11 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA f 16 " --> pdb=" O LEU f 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS f 17 " --> pdb=" O GLU f 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA f 21 " --> pdb=" O LYS f 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU f 26 " --> pdb=" O HIS f 22 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA f 28 " --> pdb=" O GLU f 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 28 removed outlier: 3.840A pdb=" N TYR g 8 " --> pdb=" O ILE g 4 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA g 9 " --> pdb=" O LEU g 5 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG g 10 " --> pdb=" O ARG g 6 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA g 14 " --> pdb=" O ARG g 10 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA g 16 " --> pdb=" O LEU g 12 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU g 19 " --> pdb=" O ASP g 15 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA g 21 " --> pdb=" O LYS g 17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU g 24 " --> pdb=" O GLU g 20 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU g 26 " --> pdb=" O HIS g 22 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA g 28 " --> pdb=" O GLU g 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 28 removed outlier: 4.025A pdb=" N TYR h 8 " --> pdb=" O ILE h 4 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA h 9 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG h 10 " --> pdb=" O ARG h 6 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA h 14 " --> pdb=" O ARG h 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP h 15 " --> pdb=" O ILE h 11 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA h 16 " --> pdb=" O LEU h 12 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS h 17 " --> pdb=" O GLU h 13 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU h 19 " --> pdb=" O ASP h 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA h 21 " --> pdb=" O LYS h 17 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU h 26 " --> pdb=" O HIS h 22 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA h 28 " --> pdb=" O GLU h 24 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 28 removed outlier: 4.099A pdb=" N TYR i 8 " --> pdb=" O ILE i 4 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA i 9 " --> pdb=" O LEU i 5 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG i 10 " --> pdb=" O ARG i 6 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA i 14 " --> pdb=" O ARG i 10 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA i 16 " --> pdb=" O LEU i 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS i 17 " --> pdb=" O GLU i 13 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU i 19 " --> pdb=" O ASP i 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA i 21 " --> pdb=" O LYS i 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU i 24 " --> pdb=" O GLU i 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU i 26 " --> pdb=" O HIS i 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA i 28 " --> pdb=" O GLU i 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 28 removed outlier: 3.795A pdb=" N TYR j 8 " --> pdb=" O ILE j 4 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA j 9 " --> pdb=" O LEU j 5 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG j 10 " --> pdb=" O ARG j 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA j 14 " --> pdb=" O ARG j 10 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA j 16 " --> pdb=" O LEU j 12 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS j 17 " --> pdb=" O GLU j 13 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU j 19 " --> pdb=" O ASP j 15 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA j 21 " --> pdb=" O LYS j 17 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU j 26 " --> pdb=" O HIS j 22 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 28 removed outlier: 3.848A pdb=" N TYR k 8 " --> pdb=" O ILE k 4 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA k 9 " --> pdb=" O LEU k 5 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG k 10 " --> pdb=" O ARG k 6 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA k 14 " --> pdb=" O ARG k 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU k 19 " --> pdb=" O ASP k 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA k 21 " --> pdb=" O LYS k 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU k 24 " --> pdb=" O GLU k 20 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU k 26 " --> pdb=" O HIS k 22 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA k 28 " --> pdb=" O GLU k 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 28 removed outlier: 4.073A pdb=" N TYR l 8 " --> pdb=" O ILE l 4 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA l 9 " --> pdb=" O LEU l 5 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG l 10 " --> pdb=" O ARG l 6 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA l 14 " --> pdb=" O ARG l 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS l 17 " --> pdb=" O GLU l 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU l 19 " --> pdb=" O ASP l 15 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU l 26 " --> pdb=" O HIS l 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA l 28 " --> pdb=" O GLU l 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 28 removed outlier: 3.871A pdb=" N TYR m 8 " --> pdb=" O ILE m 4 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA m 9 " --> pdb=" O LEU m 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG m 10 " --> pdb=" O ARG m 6 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA m 14 " --> pdb=" O ARG m 10 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA m 16 " --> pdb=" O LEU m 12 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS m 17 " --> pdb=" O GLU m 13 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE m 18 " --> pdb=" O ALA m 14 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU m 19 " --> pdb=" O ASP m 15 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA m 21 " --> pdb=" O LYS m 17 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU m 24 " --> pdb=" O GLU m 20 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU m 26 " --> pdb=" O HIS m 22 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA m 28 " --> pdb=" O GLU m 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 28 removed outlier: 3.722A pdb=" N TYR n 8 " --> pdb=" O ILE n 4 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA n 9 " --> pdb=" O LEU n 5 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG n 10 " --> pdb=" O ARG n 6 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP n 15 " --> pdb=" O ILE n 11 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA n 16 " --> pdb=" O LEU n 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS n 17 " --> pdb=" O GLU n 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU n 19 " --> pdb=" O ASP n 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU n 26 " --> pdb=" O HIS n 22 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA n 28 " --> pdb=" O GLU n 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 23 removed outlier: 4.024A pdb=" N TYR o 8 " --> pdb=" O ILE o 4 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA o 9 " --> pdb=" O LEU o 5 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG o 10 " --> pdb=" O ARG o 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA o 16 " --> pdb=" O LEU o 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS o 17 " --> pdb=" O GLU o 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU o 19 " --> pdb=" O ASP o 15 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA o 21 " --> pdb=" O LYS o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 28 removed outlier: 3.616A pdb=" N ALA o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 28 removed outlier: 4.134A pdb=" N TYR p 8 " --> pdb=" O ILE p 4 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA p 9 " --> pdb=" O LEU p 5 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG p 10 " --> pdb=" O ARG p 6 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA p 14 " --> pdb=" O ARG p 10 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP p 15 " --> pdb=" O ILE p 11 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA p 16 " --> pdb=" O LEU p 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS p 17 " --> pdb=" O GLU p 13 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU p 19 " --> pdb=" O ASP p 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA p 21 " --> pdb=" O LYS p 17 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU p 26 " --> pdb=" O HIS p 22 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA p 28 " --> pdb=" O GLU p 24 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 23 removed outlier: 3.876A pdb=" N TYR q 8 " --> pdb=" O ILE q 4 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA q 9 " --> pdb=" O LEU q 5 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG q 10 " --> pdb=" O ARG q 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA q 14 " --> pdb=" O ARG q 10 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA q 16 " --> pdb=" O LEU q 12 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS q 17 " --> pdb=" O GLU q 13 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU q 19 " --> pdb=" O ASP q 15 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA q 21 " --> pdb=" O LYS q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 23 through 28 removed outlier: 3.789A pdb=" N ALA q 28 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 25 removed outlier: 3.749A pdb=" N TYR r 8 " --> pdb=" O ILE r 4 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA r 9 " --> pdb=" O LEU r 5 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG r 10 " --> pdb=" O ARG r 6 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA r 14 " --> pdb=" O ARG r 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA r 16 " --> pdb=" O LEU r 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS r 17 " --> pdb=" O GLU r 13 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU r 19 " --> pdb=" O ASP r 15 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA r 21 " --> pdb=" O LYS r 17 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 23 removed outlier: 3.857A pdb=" N TYR s 8 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA s 9 " --> pdb=" O LEU s 5 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA s 14 " --> pdb=" O ARG s 10 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA s 16 " --> pdb=" O LEU s 12 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU s 19 " --> pdb=" O ASP s 15 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 23 through 28 removed outlier: 3.788A pdb=" N ALA s 28 " --> pdb=" O GLU s 24 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 25 removed outlier: 3.956A pdb=" N TYR t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA t 9 " --> pdb=" O LEU t 5 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA t 14 " --> pdb=" O ARG t 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA t 16 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS t 17 " --> pdb=" O GLU t 13 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU t 19 " --> pdb=" O ASP t 15 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA t 21 " --> pdb=" O LYS t 17 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 4.05 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: 106.12 - 111.22: 3676 111.22 - 116.31: 2364 116.31 - 121.41: 4568 121.41 - 126.51: 1672 126.51 - 131.60: 40 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 2.520 nonbonded pdb=" O LYS c 27 " pdb=" NH2 ARG f 10 " model vdw 2.368 2.520 nonbonded pdb=" OE1 GLN M 29 " pdb=" NH1 ARG T 6 " model vdw 2.373 2.520 nonbonded pdb=" O LYS M 27 " pdb=" NH2 ARG d 10 " model vdw 2.377 2.520 nonbonded pdb=" O LYS f 27 " pdb=" NH2 ARG m 10 " model vdw 2.377 2.520 ... (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 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 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. 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.680 Check model and map are aligned: 0.120 Process input model: 25.890 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 603 time to evaluate : 1.184 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 outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 0.2258 time to fit residues: 181.1769 Evaluate side-chains 281 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4908 ------------------------------------------------------------------------------- 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: 0.0170 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4854 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= 0.185 Angle : 0.622 4.473 12320 Z= 0.350 Chirality : 0.039 0.120 1460 Planarity : 0.003 0.018 1600 Dihedral : 5.910 29.709 1280 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 3.17 % 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: -5.25 (0.19), residues: 1080 helix: -3.10 (0.11), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 605 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 579 time to evaluate : 1.139 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 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 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 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 outliers start: 26 outliers final: 0 residues processed: 579 average time/residue: 0.2252 time to fit residues: 174.2945 Evaluate side-chains 285 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- 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 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9180 Z= 0.231 Angle : 0.634 4.629 12320 Z= 0.371 Chirality : 0.042 0.147 1460 Planarity : 0.003 0.023 1600 Dihedral : 5.978 51.525 1280 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer Outliers : 0.85 % 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: -4.31 (0.20), residues: 1080 helix: -2.51 (0.12), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 542 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 535 time to evaluate : 1.175 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 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 outliers start: 7 outliers final: 0 residues processed: 535 average time/residue: 0.2266 time to fit residues: 162.2849 Evaluate side-chains 247 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.5741 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= 0.197 Angle : 0.640 4.889 12320 Z= 0.373 Chirality : 0.041 0.141 1460 Planarity : 0.003 0.021 1600 Dihedral : 6.225 52.503 1280 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 1.34 % 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: -3.61 (0.21), residues: 1080 helix: -2.08 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 542 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 531 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "GLN g 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 outliers start: 11 outliers final: 4 residues processed: 531 average time/residue: 0.2234 time to fit residues: 158.5855 Evaluate side-chains 278 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 274 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1257 time to fit residues: 2.2648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9180 Z= 0.205 Angle : 0.670 5.439 12320 Z= 0.390 Chirality : 0.042 0.143 1460 Planarity : 0.003 0.019 1600 Dihedral : 6.359 54.313 1280 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 0.49 % 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: -3.13 (0.22), residues: 1080 helix: -1.79 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 531 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 527 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "GLN g 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 outliers start: 4 outliers final: 4 residues processed: 527 average time/residue: 0.2302 time to fit residues: 163.3146 Evaluate side-chains 277 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1140 time to fit residues: 2.2743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 0.0670 chunk 74 optimal weight: 0.9980 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9180 Z= 0.194 Angle : 0.704 5.276 12320 Z= 0.405 Chirality : 0.042 0.137 1460 Planarity : 0.002 0.020 1600 Dihedral : 6.262 53.799 1280 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer Outliers : 0.24 % 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: -2.73 (0.22), residues: 1080 helix: -1.54 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 538 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 536 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "GLN g 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 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 outliers start: 2 outliers final: 2 residues processed: 536 average time/residue: 0.2180 time to fit residues: 157.4084 Evaluate side-chains 292 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1155 time to fit residues: 1.8950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 29 GLN ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.6527 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= 0.225 Angle : 0.760 5.756 12320 Z= 0.435 Chirality : 0.045 0.183 1460 Planarity : 0.003 0.021 1600 Dihedral : 6.135 45.955 1280 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer Outliers : 0.24 % 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: -2.59 (0.22), residues: 1080 helix: -1.45 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 519 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 517 time to evaluate : 1.252 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 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 g 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 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 outliers start: 2 outliers final: 0 residues processed: 517 average time/residue: 0.2211 time to fit residues: 155.1728 Evaluate side-chains 285 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.240 Angle : 0.807 6.347 12320 Z= 0.462 Chirality : 0.045 0.167 1460 Planarity : 0.003 0.026 1600 Dihedral : 6.089 37.325 1280 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.22), residues: 1080 helix: -1.36 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 512 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 1.166 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 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 g 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.2165 time to fit residues: 149.9053 Evaluate side-chains 283 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 0.0370 overall best weight: 2.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9180 Z= 0.264 Angle : 0.856 7.152 12320 Z= 0.490 Chirality : 0.047 0.193 1460 Planarity : 0.003 0.026 1600 Dihedral : 6.197 40.085 1280 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.22), residues: 1080 helix: -1.29 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 501 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "GLN n 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 outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.2136 time to fit residues: 145.2579 Evaluate side-chains 304 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9180 Z= 0.261 Angle : 0.877 6.696 12320 Z= 0.497 Chirality : 0.047 0.190 1460 Planarity : 0.003 0.023 1600 Dihedral : 6.210 41.927 1280 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.23), residues: 1080 helix: -1.21 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 ********************** 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 500 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 1.136 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 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 TARDY: cannot create tardy model for: "GLN n 1 " (corrupted residue). Skipping it. 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 outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.2108 time to fit residues: 143.4236 Evaluate side-chains 303 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.064770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.059916 restraints weight = 58517.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.061097 restraints weight = 22787.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.061760 restraints weight = 10994.078| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9180 Z= 0.270 Angle : 0.883 6.327 12320 Z= 0.501 Chirality : 0.048 0.195 1460 Planarity : 0.003 0.022 1600 Dihedral : 6.190 43.673 1280 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 1080 helix: -1.12 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 =============================================================================== Job complete usr+sys time: 2753.67 seconds wall clock time: 50 minutes 20.88 seconds (3020.88 seconds total)