Starting phenix.real_space_refine on Wed Mar 4 05:03:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wl0_21814/03_2026/6wl0_21814.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wl0_21814/03_2026/6wl0_21814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wl0_21814/03_2026/6wl0_21814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wl0_21814/03_2026/6wl0_21814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wl0_21814/03_2026/6wl0_21814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wl0_21814/03_2026/6wl0_21814.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 7298 2.51 5 N 2009 2.21 5 O 2173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11480 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 280 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'TRANS': 35} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o Time building chain proxies: 0.91, per 1000 atoms: 0.08 Number of scatterers: 11480 At special positions: 0 Unit cell: (96.72, 96.72, 131.04, 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 2173 8.00 N 2009 7.00 C 7298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 560.2 milliseconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 97.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 36 removed outlier: 3.539A pdb=" N ALA A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA F 14 " --> pdb=" O ARG F 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA H 14 " --> pdb=" O ARG H 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE H 18 " --> pdb=" O ALA H 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA I 14 " --> pdb=" O ARG I 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE I 18 " --> pdb=" O ALA I 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 30 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU I 31 " --> pdb=" O LYS I 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU I 33 " --> pdb=" O LYS I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA J 14 " --> pdb=" O ARG J 10 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA J 16 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU J 19 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU J 31 " --> pdb=" O LYS J 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA K 14 " --> pdb=" O ARG K 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA K 16 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU K 19 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA L 14 " --> pdb=" O ARG L 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU L 19 " --> pdb=" O LYS L 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 30 " --> pdb=" O LEU L 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU L 33 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 36 removed outlier: 3.541A pdb=" N ALA M 14 " --> pdb=" O ARG M 10 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU M 17 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU M 19 " --> pdb=" O LYS M 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA M 30 " --> pdb=" O LEU M 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU M 33 " --> pdb=" O LYS M 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA N 16 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU N 17 " --> pdb=" O GLU N 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU N 19 " --> pdb=" O LYS N 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 30 " --> pdb=" O LEU N 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU N 33 " --> pdb=" O LYS N 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA O 16 " --> pdb=" O LEU O 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU O 17 " --> pdb=" O GLU O 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA O 30 " --> pdb=" O LEU O 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU O 31 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU P 17 " --> pdb=" O GLU P 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU P 19 " --> pdb=" O LYS P 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU P 26 " --> pdb=" O LYS P 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA P 30 " --> pdb=" O LEU P 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU P 33 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA Q 16 " --> pdb=" O LEU Q 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU Q 17 " --> pdb=" O GLU Q 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Q 26 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU Q 31 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Q 33 " --> pdb=" O LYS Q 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA R 14 " --> pdb=" O ARG R 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA R 16 " --> pdb=" O LEU R 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU R 17 " --> pdb=" O GLU R 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU R 19 " --> pdb=" O LYS R 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 26 " --> pdb=" O LYS R 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA R 30 " --> pdb=" O LEU R 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA S 14 " --> pdb=" O ARG S 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU S 17 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU S 19 " --> pdb=" O LYS S 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU S 26 " --> pdb=" O LYS S 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA S 30 " --> pdb=" O LEU S 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU S 33 " --> pdb=" O LYS S 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA T 14 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA T 16 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU T 26 " --> pdb=" O LYS T 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA T 30 " --> pdb=" O LEU T 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU T 31 " --> pdb=" O LYS T 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU T 33 " --> pdb=" O LYS T 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA U 14 " --> pdb=" O ARG U 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA U 16 " --> pdb=" O LEU U 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE U 18 " --> pdb=" O ALA U 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU U 19 " --> pdb=" O LYS U 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU U 26 " --> pdb=" O LYS U 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA U 30 " --> pdb=" O LEU U 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU U 31 " --> pdb=" O LYS U 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA V 14 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA V 16 " --> pdb=" O LEU V 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU V 17 " --> pdb=" O GLU V 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE V 18 " --> pdb=" O ALA V 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU V 19 " --> pdb=" O LYS V 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU V 26 " --> pdb=" O LYS V 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA V 30 " --> pdb=" O LEU V 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU V 31 " --> pdb=" O LYS V 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU V 33 " --> pdb=" O LYS V 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA W 16 " --> pdb=" O LEU W 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU W 17 " --> pdb=" O GLU W 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE W 18 " --> pdb=" O ALA W 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU W 26 " --> pdb=" O LYS W 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA W 30 " --> pdb=" O LEU W 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU W 31 " --> pdb=" O LYS W 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA X 14 " --> pdb=" O ARG X 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE X 18 " --> pdb=" O ALA X 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU X 19 " --> pdb=" O LYS X 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU X 26 " --> pdb=" O LYS X 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA X 30 " --> pdb=" O LEU X 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU X 31 " --> pdb=" O LYS X 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA Y 14 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA Y 16 " --> pdb=" O LEU Y 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU Y 17 " --> pdb=" O GLU Y 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE Y 18 " --> pdb=" O ALA Y 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Y 26 " --> pdb=" O LYS Y 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Y 30 " --> pdb=" O LEU Y 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU Y 31 " --> pdb=" O LYS Y 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA Z 14 " --> pdb=" O ARG Z 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA Z 16 " --> pdb=" O LEU Z 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU Z 17 " --> pdb=" O GLU Z 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE Z 18 " --> pdb=" O ALA Z 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU Z 19 " --> pdb=" O LYS Z 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Z 26 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Z 30 " --> pdb=" O LEU Z 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU Z 31 " --> pdb=" O LYS Z 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Z 33 " --> pdb=" O LYS Z 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA a 14 " --> pdb=" O ARG a 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU a 17 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE a 18 " --> pdb=" O ALA a 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU a 19 " --> pdb=" O LYS a 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU a 26 " --> pdb=" O LYS a 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA a 30 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU a 31 " --> pdb=" O LYS a 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU a 33 " --> pdb=" O LYS a 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA b 14 " --> pdb=" O ARG b 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA b 16 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE b 18 " --> pdb=" O ALA b 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 26 " --> pdb=" O LYS b 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA b 30 " --> pdb=" O LEU b 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU b 31 " --> pdb=" O LYS b 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU b 33 " --> pdb=" O LYS b 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA c 14 " --> pdb=" O ARG c 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA c 16 " --> pdb=" O LEU c 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE c 18 " --> pdb=" O ALA c 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU c 19 " --> pdb=" O LYS c 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU c 26 " --> pdb=" O LYS c 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA c 30 " --> pdb=" O LEU c 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU c 33 " --> pdb=" O LYS c 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA d 16 " --> pdb=" O LEU d 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU d 17 " --> pdb=" O GLU d 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU d 19 " --> pdb=" O LYS d 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU d 26 " --> pdb=" O LYS d 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA d 30 " --> pdb=" O LEU d 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU d 31 " --> pdb=" O LYS d 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU d 33 " --> pdb=" O LYS d 29 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA e 14 " --> pdb=" O ARG e 10 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA e 16 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU e 17 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE e 18 " --> pdb=" O ALA e 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU e 19 " --> pdb=" O LYS e 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU e 26 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA e 30 " --> pdb=" O LEU e 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU e 31 " --> pdb=" O LYS e 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU e 33 " --> pdb=" O LYS e 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA f 16 " --> pdb=" O LEU f 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU f 17 " --> pdb=" O GLU f 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE f 18 " --> pdb=" O ALA f 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU f 19 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU f 26 " --> pdb=" O LYS f 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA f 30 " --> pdb=" O LEU f 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA g 14 " --> pdb=" O ARG g 10 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA g 16 " --> pdb=" O LEU g 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE g 18 " --> pdb=" O ALA g 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU g 19 " --> pdb=" O LYS g 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU g 26 " --> pdb=" O LYS g 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU g 31 " --> pdb=" O LYS g 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU g 33 " --> pdb=" O LYS g 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA h 14 " --> pdb=" O ARG h 10 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA h 16 " --> pdb=" O LEU h 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU h 17 " --> pdb=" O GLU h 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE h 18 " --> pdb=" O ALA h 14 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU h 19 " --> pdb=" O LYS h 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU h 26 " --> pdb=" O LYS h 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA h 30 " --> pdb=" O LEU h 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU h 33 " --> pdb=" O LYS h 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA i 14 " --> pdb=" O ARG i 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA i 16 " --> pdb=" O LEU i 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU i 17 " --> pdb=" O GLU i 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE i 18 " --> pdb=" O ALA i 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU i 19 " --> pdb=" O LYS i 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU i 26 " --> pdb=" O LYS i 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA i 30 " --> pdb=" O LEU i 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU i 31 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU i 33 " --> pdb=" O LYS i 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA j 14 " --> pdb=" O ARG j 10 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA j 16 " --> pdb=" O LEU j 12 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU j 17 " --> pdb=" O GLU j 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE j 18 " --> pdb=" O ALA j 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU j 19 " --> pdb=" O LYS j 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU j 26 " --> pdb=" O LYS j 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA j 30 " --> pdb=" O LEU j 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU j 31 " --> pdb=" O LYS j 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU j 33 " --> pdb=" O LYS j 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA k 14 " --> pdb=" O ARG k 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE k 18 " --> pdb=" O ALA k 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU k 19 " --> pdb=" O LYS k 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU k 26 " --> pdb=" O LYS k 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA k 30 " --> pdb=" O LEU k 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU k 31 " --> pdb=" O LYS k 27 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU k 33 " --> pdb=" O LYS k 29 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 36 removed outlier: 3.539A pdb=" N ALA l 14 " --> pdb=" O ARG l 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU l 17 " --> pdb=" O GLU l 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE l 18 " --> pdb=" O ALA l 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU l 19 " --> pdb=" O LYS l 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU l 26 " --> pdb=" O LYS l 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA l 30 " --> pdb=" O LEU l 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU l 31 " --> pdb=" O LYS l 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU l 33 " --> pdb=" O LYS l 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA m 14 " --> pdb=" O ARG m 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA m 16 " --> pdb=" O LEU m 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU m 17 " --> pdb=" O GLU m 13 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE m 18 " --> pdb=" O ALA m 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU m 19 " --> pdb=" O LYS m 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU m 26 " --> pdb=" O LYS m 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA m 30 " --> pdb=" O LEU m 26 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU m 31 " --> pdb=" O LYS m 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU m 33 " --> pdb=" O LYS m 29 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA n 16 " --> pdb=" O LEU n 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU n 17 " --> pdb=" O GLU n 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE n 18 " --> pdb=" O ALA n 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU n 19 " --> pdb=" O LYS n 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU n 26 " --> pdb=" O LYS n 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA n 30 " --> pdb=" O LEU n 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU n 31 " --> pdb=" O LYS n 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU n 33 " --> pdb=" O LYS n 29 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 36 removed outlier: 3.540A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA o 16 " --> pdb=" O LEU o 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU o 17 " --> pdb=" O GLU o 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU o 19 " --> pdb=" O LYS o 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU o 26 " --> pdb=" O LYS o 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA o 30 " --> pdb=" O LEU o 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU o 31 " --> pdb=" O LYS o 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU o 33 " --> pdb=" O LYS o 29 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2709 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: 1.59 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2132 1.29 - 1.36: 1722 1.36 - 1.42: 0 1.42 - 1.48: 1603 1.48 - 1.55: 5982 Bond restraints: 11439 Sorted by residual: bond pdb=" CB ARG I 6 " pdb=" CG ARG I 6 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.68e-01 bond pdb=" CB ARG V 6 " pdb=" CG ARG V 6 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.67e-01 bond pdb=" CB ARG J 6 " pdb=" CG ARG J 6 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.61e-01 bond pdb=" CB ARG i 6 " pdb=" CG ARG i 6 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.52e-01 bond pdb=" CB ARG a 6 " pdb=" CG ARG a 6 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.52e-01 ... (remaining 11434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.71: 11476 0.71 - 1.42: 2624 1.42 - 2.13: 547 2.13 - 2.84: 323 2.84 - 3.55: 241 Bond angle restraints: 15211 Sorted by residual: angle pdb=" N LYS A 34 " pdb=" CA LYS A 34 " pdb=" C LYS A 34 " ideal model delta sigma weight residual 114.04 111.33 2.71 1.24e+00 6.50e-01 4.76e+00 angle pdb=" N LYS L 34 " pdb=" CA LYS L 34 " pdb=" C LYS L 34 " ideal model delta sigma weight residual 114.04 111.34 2.70 1.24e+00 6.50e-01 4.74e+00 angle pdb=" N LYS f 34 " pdb=" CA LYS f 34 " pdb=" C LYS f 34 " ideal model delta sigma weight residual 114.04 111.36 2.68 1.24e+00 6.50e-01 4.69e+00 angle pdb=" N LYS J 34 " pdb=" CA LYS J 34 " pdb=" C LYS J 34 " ideal model delta sigma weight residual 114.04 111.36 2.68 1.24e+00 6.50e-01 4.69e+00 angle pdb=" N LYS n 34 " pdb=" CA LYS n 34 " pdb=" C LYS n 34 " ideal model delta sigma weight residual 114.04 111.36 2.68 1.24e+00 6.50e-01 4.69e+00 ... (remaining 15206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.29: 6014 14.29 - 28.57: 1202 28.57 - 42.86: 164 42.86 - 57.14: 123 57.14 - 71.43: 123 Dihedral angle restraints: 7626 sinusoidal: 3239 harmonic: 4387 Sorted by residual: dihedral pdb=" CA GLU K 24 " pdb=" C GLU K 24 " pdb=" N VAL K 25 " pdb=" CA VAL K 25 " ideal model delta harmonic sigma weight residual 180.00 164.73 15.27 0 5.00e+00 4.00e-02 9.33e+00 dihedral pdb=" CA GLU g 24 " pdb=" C GLU g 24 " pdb=" N VAL g 25 " pdb=" CA VAL g 25 " ideal model delta harmonic sigma weight residual 180.00 164.73 15.27 0 5.00e+00 4.00e-02 9.32e+00 dihedral pdb=" CA GLU F 24 " pdb=" C GLU F 24 " pdb=" N VAL F 25 " pdb=" CA VAL F 25 " ideal model delta harmonic sigma weight residual 180.00 164.73 15.27 0 5.00e+00 4.00e-02 9.32e+00 ... (remaining 7623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1162 0.032 - 0.065: 481 0.065 - 0.097: 243 0.097 - 0.129: 0 0.129 - 0.162: 41 Chirality restraints: 1927 Sorted by residual: chirality pdb=" CB ILE S 11 " pdb=" CA ILE S 11 " pdb=" CG1 ILE S 11 " pdb=" CG2 ILE S 11 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB ILE j 11 " pdb=" CA ILE j 11 " pdb=" CG1 ILE j 11 " pdb=" CG2 ILE j 11 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB ILE U 11 " pdb=" CA ILE U 11 " pdb=" CG1 ILE U 11 " pdb=" CG2 ILE U 11 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1924 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS o 34 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C LYS o 34 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS o 34 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA o 35 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS V 34 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.14e+00 pdb=" C LYS V 34 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS V 34 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA V 35 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS i 34 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.14e+00 pdb=" C LYS i 34 " -0.018 2.00e-02 2.50e+03 pdb=" O LYS i 34 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA i 35 " 0.006 2.00e-02 2.50e+03 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3775 2.86 - 3.37: 12626 3.37 - 3.88: 19225 3.88 - 4.39: 22863 4.39 - 4.90: 35027 Nonbonded interactions: 93516 Sorted by model distance: nonbonded pdb=" NH2 ARG M 10 " pdb=" OE1 GLU M 13 " model vdw 2.353 3.120 nonbonded pdb=" NH2 ARG R 10 " pdb=" OE1 GLU R 13 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG J 10 " pdb=" OE1 GLU J 13 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG l 10 " pdb=" OE1 GLU l 13 " model vdw 2.354 3.120 nonbonded pdb=" NH2 ARG F 10 " pdb=" OE1 GLU F 13 " model vdw 2.354 3.120 ... (remaining 93511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 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 0.025 11439 Z= 0.281 Angle : 0.822 3.549 15211 Z= 0.482 Chirality : 0.043 0.162 1927 Planarity : 0.004 0.011 1886 Dihedral : 18.907 71.429 4674 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.48 (0.17), residues: 1394 helix: -3.43 (0.10), residues: 1312 sheet: None (None), residues: 0 loop : -0.34 (0.85), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG a 6 Details of bonding type rmsd covalent geometry : bond 0.00593 (11439) covalent geometry : angle 0.82178 (15211) hydrogen bonds : bond 0.29478 ( 903) hydrogen bonds : angle 9.10174 ( 2709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8783 (mp0) cc_final: 0.8163 (mm-30) REVERT: A 10 ARG cc_start: 0.8750 (tpm170) cc_final: 0.8266 (tpm170) REVERT: A 32 ILE cc_start: 0.9162 (mt) cc_final: 0.8799 (mm) REVERT: B 27 LYS cc_start: 0.9399 (tmtt) cc_final: 0.9193 (tptp) REVERT: B 31 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9080 (mm-30) REVERT: C 19 LEU cc_start: 0.9524 (mt) cc_final: 0.9309 (mp) REVERT: C 31 GLU cc_start: 0.9388 (mm-30) cc_final: 0.8990 (mm-30) REVERT: D 2 LEU cc_start: 0.9049 (mp) cc_final: 0.8812 (mt) REVERT: D 3 GLU cc_start: 0.9068 (mp0) cc_final: 0.8786 (mp0) REVERT: D 10 ARG cc_start: 0.8964 (tpm170) cc_final: 0.7933 (tpm170) REVERT: D 13 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8441 (tm-30) REVERT: D 31 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8981 (mm-30) REVERT: E 31 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8990 (mm-30) REVERT: E 32 ILE cc_start: 0.9258 (mt) cc_final: 0.8907 (mm) REVERT: F 3 GLU cc_start: 0.8613 (mp0) cc_final: 0.8114 (mm-30) REVERT: F 10 ARG cc_start: 0.8686 (tpm170) cc_final: 0.8033 (tpm170) REVERT: F 13 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8428 (tm-30) REVERT: F 36 GLN cc_start: 0.8232 (mt0) cc_final: 0.7914 (pt0) REVERT: G 10 ARG cc_start: 0.8694 (tpm170) cc_final: 0.8247 (tpm170) REVERT: H 27 LYS cc_start: 0.9437 (tmtt) cc_final: 0.9083 (tptp) REVERT: H 31 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8960 (mm-30) REVERT: I 13 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8445 (tm-30) REVERT: I 31 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8909 (mm-30) REVERT: K 10 ARG cc_start: 0.8808 (tpm170) cc_final: 0.7827 (tpm170) REVERT: K 13 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8391 (tm-30) REVERT: L 10 ARG cc_start: 0.8699 (tpm170) cc_final: 0.8310 (tpm170) REVERT: M 3 GLU cc_start: 0.8883 (mp0) cc_final: 0.8330 (mm-30) REVERT: M 10 ARG cc_start: 0.8748 (tpm170) cc_final: 0.8374 (tpm170) REVERT: P 3 GLU cc_start: 0.8578 (mp0) cc_final: 0.7742 (mp0) REVERT: P 10 ARG cc_start: 0.8723 (tpm170) cc_final: 0.8388 (tpm170) REVERT: Q 10 ARG cc_start: 0.8630 (tpm170) cc_final: 0.8261 (tpm170) REVERT: R 10 ARG cc_start: 0.8493 (tpm170) cc_final: 0.7771 (tpm170) REVERT: R 36 GLN cc_start: 0.7780 (mt0) cc_final: 0.7335 (pt0) REVERT: S 3 GLU cc_start: 0.8650 (mp0) cc_final: 0.8287 (mm-30) REVERT: S 10 ARG cc_start: 0.8758 (tpm170) cc_final: 0.7913 (tpm170) REVERT: S 12 LEU cc_start: 0.9656 (mt) cc_final: 0.9456 (mm) REVERT: S 29 LYS cc_start: 0.9390 (tptt) cc_final: 0.9156 (tppt) REVERT: T 10 ARG cc_start: 0.8624 (tpm170) cc_final: 0.8246 (tpm170) REVERT: U 10 ARG cc_start: 0.8863 (tpm170) cc_final: 0.8418 (tpm170) REVERT: U 31 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8766 (mm-30) REVERT: V 3 GLU cc_start: 0.8776 (mp0) cc_final: 0.8008 (mp0) REVERT: V 10 ARG cc_start: 0.8673 (tpm170) cc_final: 0.8276 (tpm170) REVERT: V 12 LEU cc_start: 0.9595 (mt) cc_final: 0.9369 (mm) REVERT: V 36 GLN cc_start: 0.8194 (mt0) cc_final: 0.7974 (mt0) REVERT: W 3 GLU cc_start: 0.8721 (mp0) cc_final: 0.8387 (mm-30) REVERT: W 10 ARG cc_start: 0.8805 (tpm170) cc_final: 0.8523 (tpm170) REVERT: W 29 LYS cc_start: 0.9258 (tptt) cc_final: 0.9028 (tppt) REVERT: X 10 ARG cc_start: 0.8459 (tpm170) cc_final: 0.8117 (tpm170) REVERT: X 17 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9102 (mm-30) REVERT: X 32 ILE cc_start: 0.9451 (mt) cc_final: 0.9192 (tp) REVERT: Y 3 GLU cc_start: 0.8574 (mp0) cc_final: 0.8117 (mm-30) REVERT: Y 10 ARG cc_start: 0.8739 (tpm170) cc_final: 0.8427 (tpm170) REVERT: Z 10 ARG cc_start: 0.8651 (tpm170) cc_final: 0.8244 (tpm170) REVERT: Z 36 GLN cc_start: 0.8595 (mt0) cc_final: 0.8291 (pt0) REVERT: a 3 GLU cc_start: 0.8566 (mp0) cc_final: 0.8075 (mm-30) REVERT: a 33 LEU cc_start: 0.8055 (mt) cc_final: 0.7442 (mt) REVERT: b 10 ARG cc_start: 0.8764 (tpm170) cc_final: 0.7836 (tpm170) REVERT: b 13 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8209 (tm-30) REVERT: c 3 GLU cc_start: 0.8652 (mp0) cc_final: 0.8290 (mm-30) REVERT: d 10 ARG cc_start: 0.8531 (tpm170) cc_final: 0.8098 (tpm170) REVERT: d 17 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9090 (mm-30) REVERT: d 32 ILE cc_start: 0.9417 (mt) cc_final: 0.9196 (tp) REVERT: d 36 GLN cc_start: 0.8182 (mt0) cc_final: 0.7874 (pt0) REVERT: e 3 GLU cc_start: 0.8903 (mp0) cc_final: 0.8155 (mm-30) REVERT: f 27 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9227 (tptp) REVERT: f 31 GLU cc_start: 0.9465 (mm-30) cc_final: 0.8957 (mm-30) REVERT: g 3 GLU cc_start: 0.8862 (mp0) cc_final: 0.8556 (mp0) REVERT: h 10 ARG cc_start: 0.8667 (tpm170) cc_final: 0.8343 (tpm170) REVERT: i 3 GLU cc_start: 0.8575 (mp0) cc_final: 0.8333 (mm-30) REVERT: i 29 LYS cc_start: 0.9244 (tptt) cc_final: 0.8856 (tppt) REVERT: j 10 ARG cc_start: 0.8650 (tpm170) cc_final: 0.8242 (tpm170) REVERT: j 29 LYS cc_start: 0.9437 (tptt) cc_final: 0.9089 (tmmt) REVERT: k 3 GLU cc_start: 0.8648 (mp0) cc_final: 0.8257 (mm-30) REVERT: l 19 LEU cc_start: 0.9265 (mt) cc_final: 0.8761 (tt) REVERT: l 29 LYS cc_start: 0.9415 (tptt) cc_final: 0.9111 (tmmt) REVERT: l 31 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9044 (mm-30) REVERT: n 10 ARG cc_start: 0.8712 (tpm170) cc_final: 0.8230 (tpm170) REVERT: o 3 GLU cc_start: 0.8502 (mp0) cc_final: 0.8133 (mm-30) REVERT: o 32 ILE cc_start: 0.9097 (mt) cc_final: 0.8763 (tp) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.1839 time to fit residues: 154.2931 Evaluate side-chains 394 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 0.4980 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 36 GLN m 36 GLN o 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054707 restraints weight = 53299.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055919 restraints weight = 36779.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.056894 restraints weight = 27992.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057579 restraints weight = 22178.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.058129 restraints weight = 18420.578| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11439 Z= 0.198 Angle : 0.686 6.660 15211 Z= 0.372 Chirality : 0.034 0.110 1927 Planarity : 0.004 0.028 1886 Dihedral : 6.807 34.345 1558 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.45 % Allowed : 10.66 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.21), residues: 1394 helix: -1.23 (0.13), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 10 Details of bonding type rmsd covalent geometry : bond 0.00418 (11439) covalent geometry : angle 0.68579 (15211) hydrogen bonds : bond 0.04954 ( 903) hydrogen bonds : angle 5.43798 ( 2709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 568 time to evaluate : 0.497 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: D 3 GLU cc_start: 0.8629 (mp0) cc_final: 0.8384 (mm-30) REVERT: E 29 LYS cc_start: 0.9400 (mmpt) cc_final: 0.9119 (mmmt) REVERT: E 31 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8277 (mm-30) REVERT: G 3 GLU cc_start: 0.8755 (mp0) cc_final: 0.8366 (mp0) REVERT: H 5 LEU cc_start: 0.9443 (mt) cc_final: 0.9225 (mm) REVERT: I 32 ILE cc_start: 0.9185 (mm) cc_final: 0.8676 (mt) REVERT: J 3 GLU cc_start: 0.8380 (mp0) cc_final: 0.8028 (mp0) REVERT: J 29 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9143 (mmmt) REVERT: K 5 LEU cc_start: 0.9484 (mt) cc_final: 0.9279 (mm) REVERT: K 31 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8707 (mm-30) REVERT: M 3 GLU cc_start: 0.8493 (mp0) cc_final: 0.8201 (tp30) REVERT: N 5 LEU cc_start: 0.9428 (mt) cc_final: 0.9219 (mm) REVERT: P 3 GLU cc_start: 0.8277 (mp0) cc_final: 0.7593 (mp0) REVERT: R 12 LEU cc_start: 0.9531 (tt) cc_final: 0.9130 (tp) REVERT: U 29 LYS cc_start: 0.9249 (mmpt) cc_final: 0.8915 (tppt) REVERT: V 12 LEU cc_start: 0.9650 (mt) cc_final: 0.8917 (mt) REVERT: V 36 GLN cc_start: 0.8268 (mt0) cc_final: 0.7917 (tt0) REVERT: f 10 ARG cc_start: 0.8633 (mmp80) cc_final: 0.8357 (mmp80) REVERT: f 29 LYS cc_start: 0.9442 (tppt) cc_final: 0.9203 (mmmt) REVERT: j 3 GLU cc_start: 0.8814 (mp0) cc_final: 0.8152 (mp0) REVERT: j 5 LEU cc_start: 0.9330 (mt) cc_final: 0.9108 (mm) REVERT: j 29 LYS cc_start: 0.9308 (tptt) cc_final: 0.8899 (tmmt) REVERT: k 24 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8868 (mm-30) REVERT: l 19 LEU cc_start: 0.9307 (mt) cc_final: 0.8724 (tp) REVERT: l 29 LYS cc_start: 0.9240 (tptt) cc_final: 0.8949 (tmmt) REVERT: m 5 LEU cc_start: 0.9475 (mt) cc_final: 0.9254 (mm) REVERT: n 29 LYS cc_start: 0.9338 (mmtt) cc_final: 0.8974 (tmmt) REVERT: o 24 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9071 (mm-30) outliers start: 5 outliers final: 1 residues processed: 568 average time/residue: 0.1870 time to fit residues: 131.7817 Evaluate side-chains 422 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN N 36 GLN P 36 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.093179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.084382 restraints weight = 62495.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.085720 restraints weight = 34172.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086602 restraints weight = 22006.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.087212 restraints weight = 15593.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.087649 restraints weight = 11883.931| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11439 Z= 0.162 Angle : 0.624 9.680 15211 Z= 0.335 Chirality : 0.034 0.117 1927 Planarity : 0.004 0.044 1886 Dihedral : 5.338 30.535 1558 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.54 % Allowed : 5.51 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1394 helix: -0.27 (0.13), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 6 Details of bonding type rmsd covalent geometry : bond 0.00351 (11439) covalent geometry : angle 0.62402 (15211) hydrogen bonds : bond 0.04124 ( 903) hydrogen bonds : angle 4.99884 ( 2709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 562 time to evaluate : 0.472 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: B 36 GLN cc_start: 0.6056 (OUTLIER) cc_final: 0.5479 (pp30) REVERT: C 3 GLU cc_start: 0.8633 (mp0) cc_final: 0.8419 (mm-30) REVERT: D 3 GLU cc_start: 0.8704 (mp0) cc_final: 0.8451 (mm-30) REVERT: E 27 LYS cc_start: 0.9284 (tmtt) cc_final: 0.8998 (tptp) REVERT: E 31 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8624 (mm-30) REVERT: H 5 LEU cc_start: 0.9382 (mt) cc_final: 0.9111 (mm) REVERT: H 29 LYS cc_start: 0.9444 (tppt) cc_final: 0.9193 (mmmt) REVERT: H 32 ILE cc_start: 0.9115 (mt) cc_final: 0.8910 (pt) REVERT: H 36 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5798 (pp30) REVERT: I 29 LYS cc_start: 0.9340 (mmmt) cc_final: 0.8898 (mmmt) REVERT: K 29 LYS cc_start: 0.9332 (mmmt) cc_final: 0.9130 (mmmt) REVERT: L 3 GLU cc_start: 0.8732 (mp0) cc_final: 0.8500 (mm-30) REVERT: L 29 LYS cc_start: 0.9271 (mmtt) cc_final: 0.9047 (mmmt) REVERT: N 3 GLU cc_start: 0.8478 (mp0) cc_final: 0.8097 (mp0) REVERT: N 5 LEU cc_start: 0.9401 (mt) cc_final: 0.9125 (mm) REVERT: N 29 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8912 (mmmt) REVERT: P 36 GLN cc_start: 0.6193 (OUTLIER) cc_final: 0.5933 (pp30) REVERT: S 3 GLU cc_start: 0.8407 (mp0) cc_final: 0.8151 (tp30) REVERT: T 3 GLU cc_start: 0.8568 (mp0) cc_final: 0.8362 (mm-30) REVERT: W 24 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8544 (mm-30) REVERT: X 36 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.4827 (pp30) REVERT: b 34 LYS cc_start: 0.8274 (tppt) cc_final: 0.7019 (tppt) REVERT: d 3 GLU cc_start: 0.8758 (mp0) cc_final: 0.8172 (mp0) REVERT: e 3 GLU cc_start: 0.8815 (mp0) cc_final: 0.8280 (tp30) REVERT: j 5 LEU cc_start: 0.9384 (mt) cc_final: 0.8998 (mm) REVERT: j 29 LYS cc_start: 0.9294 (tptt) cc_final: 0.8933 (tmmt) REVERT: l 3 GLU cc_start: 0.8509 (mp0) cc_final: 0.8294 (mp0) REVERT: l 19 LEU cc_start: 0.9291 (mt) cc_final: 0.8701 (tp) REVERT: l 29 LYS cc_start: 0.9219 (tptt) cc_final: 0.8948 (tmmt) REVERT: m 5 LEU cc_start: 0.9460 (mt) cc_final: 0.9231 (mm) REVERT: n 5 LEU cc_start: 0.9390 (mt) cc_final: 0.9071 (mm) REVERT: n 29 LYS cc_start: 0.9251 (mmtt) cc_final: 0.8909 (tmmt) outliers start: 6 outliers final: 0 residues processed: 563 average time/residue: 0.1918 time to fit residues: 133.0035 Evaluate side-chains 426 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 422 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN D 36 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.068421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.059090 restraints weight = 51012.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.060536 restraints weight = 35197.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061628 restraints weight = 26165.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.062468 restraints weight = 20563.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063108 restraints weight = 16777.990| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.7021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11439 Z= 0.156 Angle : 0.626 8.482 15211 Z= 0.337 Chirality : 0.034 0.177 1927 Planarity : 0.004 0.061 1886 Dihedral : 5.271 66.134 1558 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.45 % Allowed : 3.88 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1394 helix: 0.31 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG n 10 Details of bonding type rmsd covalent geometry : bond 0.00341 (11439) covalent geometry : angle 0.62563 (15211) hydrogen bonds : bond 0.03682 ( 903) hydrogen bonds : angle 4.91941 ( 2709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 542 time to evaluate : 0.500 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: C 3 GLU cc_start: 0.8838 (mp0) cc_final: 0.8522 (mm-30) REVERT: D 3 GLU cc_start: 0.8781 (mp0) cc_final: 0.8386 (mm-30) REVERT: E 29 LYS cc_start: 0.9383 (mmmt) cc_final: 0.8877 (mmmt) REVERT: E 32 ILE cc_start: 0.9015 (mm) cc_final: 0.8631 (mm) REVERT: F 29 LYS cc_start: 0.9352 (mmmt) cc_final: 0.8972 (mmmt) REVERT: G 29 LYS cc_start: 0.9420 (mmmt) cc_final: 0.8999 (mmmt) REVERT: I 29 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9089 (mmmt) REVERT: I 32 ILE cc_start: 0.9022 (mt) cc_final: 0.8758 (mt) REVERT: L 36 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.5778 (pp30) REVERT: N 29 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9202 (mmmt) REVERT: O 29 LYS cc_start: 0.9449 (mmpt) cc_final: 0.9098 (mmmt) REVERT: P 3 GLU cc_start: 0.8873 (mp0) cc_final: 0.8077 (mp0) REVERT: P 29 LYS cc_start: 0.9359 (mmmt) cc_final: 0.9112 (mmmt) REVERT: Q 29 LYS cc_start: 0.9381 (mmmt) cc_final: 0.9167 (mmmt) REVERT: S 3 GLU cc_start: 0.8605 (mp0) cc_final: 0.8224 (tp30) REVERT: U 10 ARG cc_start: 0.8928 (mmm160) cc_final: 0.8188 (mmm160) REVERT: Z 10 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.8424 (mtp-110) REVERT: e 3 GLU cc_start: 0.8855 (mp0) cc_final: 0.8361 (mm-30) REVERT: f 3 GLU cc_start: 0.8947 (mp0) cc_final: 0.8408 (mm-30) REVERT: j 5 LEU cc_start: 0.9377 (mt) cc_final: 0.9057 (mm) REVERT: j 29 LYS cc_start: 0.9326 (tptt) cc_final: 0.8911 (tmmt) REVERT: l 19 LEU cc_start: 0.9286 (mt) cc_final: 0.8655 (tp) REVERT: l 29 LYS cc_start: 0.9355 (tptt) cc_final: 0.8942 (tmmt) REVERT: m 29 LYS cc_start: 0.8970 (mmpt) cc_final: 0.8729 (mmmt) REVERT: n 5 LEU cc_start: 0.9332 (mt) cc_final: 0.9044 (mm) REVERT: n 10 ARG cc_start: 0.8455 (ttt90) cc_final: 0.8148 (mmm160) REVERT: n 29 LYS cc_start: 0.9272 (mmtt) cc_final: 0.8880 (tmmt) outliers start: 5 outliers final: 0 residues processed: 542 average time/residue: 0.1936 time to fit residues: 128.9479 Evaluate side-chains 411 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 0.0770 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN D 36 GLN H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057935 restraints weight = 52073.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.059183 restraints weight = 36083.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060207 restraints weight = 27535.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060999 restraints weight = 21750.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061445 restraints weight = 17848.110| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11439 Z= 0.165 Angle : 0.665 8.056 15211 Z= 0.358 Chirality : 0.036 0.137 1927 Planarity : 0.004 0.057 1886 Dihedral : 5.548 73.230 1558 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 4.52 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1394 helix: 0.72 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 10 Details of bonding type rmsd covalent geometry : bond 0.00363 (11439) covalent geometry : angle 0.66487 (15211) hydrogen bonds : bond 0.03629 ( 903) hydrogen bonds : angle 5.01634 ( 2709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 503 time to evaluate : 0.467 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: B 36 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5144 (pp30) REVERT: C 3 GLU cc_start: 0.8779 (mp0) cc_final: 0.8502 (mm-30) REVERT: D 3 GLU cc_start: 0.8710 (mp0) cc_final: 0.8436 (mp0) REVERT: D 29 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9151 (mmmt) REVERT: F 29 LYS cc_start: 0.9448 (mmmt) cc_final: 0.8995 (mmmt) REVERT: G 29 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9117 (mmtp) REVERT: H 5 LEU cc_start: 0.9303 (mt) cc_final: 0.9029 (mm) REVERT: L 3 GLU cc_start: 0.8824 (mp0) cc_final: 0.8615 (mm-30) REVERT: P 29 LYS cc_start: 0.9342 (mmmt) cc_final: 0.9036 (tppt) REVERT: P 36 GLN cc_start: 0.8389 (pt0) cc_final: 0.8059 (pp30) REVERT: Q 29 LYS cc_start: 0.9410 (mmmt) cc_final: 0.8980 (mmtp) REVERT: Q 32 ILE cc_start: 0.8974 (mt) cc_final: 0.8467 (tp) REVERT: S 3 GLU cc_start: 0.8616 (mp0) cc_final: 0.8249 (tp30) REVERT: U 10 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8340 (mmm160) REVERT: V 36 GLN cc_start: 0.6228 (pp30) cc_final: 0.5944 (pp30) REVERT: X 29 LYS cc_start: 0.9421 (mmmt) cc_final: 0.8987 (mmtp) REVERT: Z 10 ARG cc_start: 0.8706 (mtp-110) cc_final: 0.8433 (mtp-110) REVERT: b 3 GLU cc_start: 0.8785 (mp0) cc_final: 0.8562 (mp0) REVERT: e 3 GLU cc_start: 0.8921 (mp0) cc_final: 0.8407 (mm-30) REVERT: f 3 GLU cc_start: 0.8768 (mp0) cc_final: 0.8445 (mm-30) REVERT: g 29 LYS cc_start: 0.9502 (tppt) cc_final: 0.9286 (tppt) REVERT: h 29 LYS cc_start: 0.9370 (mmpt) cc_final: 0.8842 (mmmt) REVERT: i 29 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8849 (mmmt) REVERT: j 5 LEU cc_start: 0.9326 (mt) cc_final: 0.9086 (mm) REVERT: j 29 LYS cc_start: 0.9285 (tptt) cc_final: 0.8751 (tmmt) REVERT: l 3 GLU cc_start: 0.8884 (mp0) cc_final: 0.8674 (mm-30) REVERT: l 19 LEU cc_start: 0.9266 (mt) cc_final: 0.8582 (tp) REVERT: l 29 LYS cc_start: 0.9335 (tptt) cc_final: 0.8976 (tmmt) REVERT: n 5 LEU cc_start: 0.9333 (mt) cc_final: 0.9065 (mm) REVERT: n 29 LYS cc_start: 0.9234 (mmtt) cc_final: 0.8840 (tmmt) outliers start: 3 outliers final: 0 residues processed: 503 average time/residue: 0.1824 time to fit residues: 112.5433 Evaluate side-chains 378 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN H 36 GLN L 36 GLN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN b 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.066395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057669 restraints weight = 52564.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.058933 restraints weight = 36354.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059952 restraints weight = 27689.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060567 restraints weight = 21814.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061226 restraints weight = 18409.842| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11439 Z= 0.175 Angle : 0.719 10.571 15211 Z= 0.385 Chirality : 0.037 0.162 1927 Planarity : 0.003 0.042 1886 Dihedral : 5.738 72.217 1558 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.45 % Allowed : 3.25 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1394 helix: 0.77 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 6 Details of bonding type rmsd covalent geometry : bond 0.00389 (11439) covalent geometry : angle 0.71919 (15211) hydrogen bonds : bond 0.03642 ( 903) hydrogen bonds : angle 5.19803 ( 2709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 479 time to evaluate : 0.464 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: C 3 GLU cc_start: 0.8753 (mp0) cc_final: 0.8470 (mm-30) REVERT: D 3 GLU cc_start: 0.8555 (mp0) cc_final: 0.8261 (mp0) REVERT: G 29 LYS cc_start: 0.9383 (mmmt) cc_final: 0.8957 (mmmt) REVERT: N 29 LYS cc_start: 0.9380 (mmpt) cc_final: 0.9141 (mmmt) REVERT: P 3 GLU cc_start: 0.8872 (mp0) cc_final: 0.8199 (mp0) REVERT: Q 29 LYS cc_start: 0.9427 (mmmt) cc_final: 0.9083 (mmtp) REVERT: S 3 GLU cc_start: 0.8602 (mp0) cc_final: 0.8284 (mm-30) REVERT: X 29 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9029 (mmtp) REVERT: Z 5 LEU cc_start: 0.9360 (mm) cc_final: 0.9150 (mm) REVERT: e 3 GLU cc_start: 0.8811 (mp0) cc_final: 0.8330 (mm-30) REVERT: f 3 GLU cc_start: 0.8678 (mp0) cc_final: 0.8334 (mm-30) REVERT: h 29 LYS cc_start: 0.9326 (mmpt) cc_final: 0.8882 (mmmt) REVERT: j 5 LEU cc_start: 0.9315 (mt) cc_final: 0.9016 (mm) REVERT: j 29 LYS cc_start: 0.9297 (tptt) cc_final: 0.8766 (tmmt) REVERT: l 19 LEU cc_start: 0.9245 (mt) cc_final: 0.8567 (tp) REVERT: l 29 LYS cc_start: 0.9301 (tptt) cc_final: 0.8957 (tmmt) REVERT: n 29 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8812 (tmmt) outliers start: 5 outliers final: 1 residues processed: 480 average time/residue: 0.1879 time to fit residues: 111.0269 Evaluate side-chains 369 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN D 36 GLN E 36 GLN H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057205 restraints weight = 52779.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.058563 restraints weight = 36117.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059560 restraints weight = 26861.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.060290 restraints weight = 21112.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060905 restraints weight = 17438.922| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11439 Z= 0.185 Angle : 0.757 9.129 15211 Z= 0.407 Chirality : 0.038 0.278 1927 Planarity : 0.003 0.043 1886 Dihedral : 5.693 74.759 1558 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 2.71 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1394 helix: 0.72 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG l 6 Details of bonding type rmsd covalent geometry : bond 0.00407 (11439) covalent geometry : angle 0.75701 (15211) hydrogen bonds : bond 0.03673 ( 903) hydrogen bonds : angle 5.36409 ( 2709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 473 time to evaluate : 0.460 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: B 36 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.5581 (pp30) REVERT: C 3 GLU cc_start: 0.8826 (mp0) cc_final: 0.8501 (mm-30) REVERT: D 3 GLU cc_start: 0.8608 (mp0) cc_final: 0.8252 (mp0) REVERT: G 29 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9122 (mmtp) REVERT: L 24 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8722 (mm-30) REVERT: L 27 LYS cc_start: 0.9140 (tmmt) cc_final: 0.8902 (ttpp) REVERT: N 29 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9141 (mmmt) REVERT: N 32 ILE cc_start: 0.9204 (mm) cc_final: 0.8990 (mm) REVERT: P 3 GLU cc_start: 0.8929 (mp0) cc_final: 0.8700 (mp0) REVERT: Q 29 LYS cc_start: 0.9382 (mmmt) cc_final: 0.9085 (mmtp) REVERT: S 3 GLU cc_start: 0.8530 (mp0) cc_final: 0.8231 (tp30) REVERT: T 29 LYS cc_start: 0.9376 (mmmt) cc_final: 0.9142 (mmmt) REVERT: X 29 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9135 (mmtp) REVERT: d 10 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8255 (mmm160) REVERT: e 3 GLU cc_start: 0.8842 (mp0) cc_final: 0.8342 (mm-30) REVERT: f 3 GLU cc_start: 0.8755 (mp0) cc_final: 0.8362 (mm-30) REVERT: h 29 LYS cc_start: 0.9349 (mmpt) cc_final: 0.8968 (mmmt) REVERT: j 5 LEU cc_start: 0.9321 (mt) cc_final: 0.9075 (mm) REVERT: j 29 LYS cc_start: 0.9293 (tptt) cc_final: 0.8713 (tmmt) REVERT: l 19 LEU cc_start: 0.9208 (mt) cc_final: 0.8631 (tt) REVERT: l 29 LYS cc_start: 0.9280 (tptt) cc_final: 0.8870 (tmmt) REVERT: n 29 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8836 (tmmt) outliers start: 4 outliers final: 1 residues processed: 474 average time/residue: 0.1934 time to fit residues: 112.7616 Evaluate side-chains 375 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.059126 restraints weight = 51749.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.060513 restraints weight = 35399.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061581 restraints weight = 26536.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.062371 restraints weight = 20885.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062989 restraints weight = 17149.474| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.8154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11439 Z= 0.173 Angle : 0.785 8.768 15211 Z= 0.422 Chirality : 0.039 0.209 1927 Planarity : 0.004 0.123 1886 Dihedral : 5.630 70.587 1558 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.36 % Allowed : 2.44 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1394 helix: 0.68 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 10 Details of bonding type rmsd covalent geometry : bond 0.00387 (11439) covalent geometry : angle 0.78544 (15211) hydrogen bonds : bond 0.03766 ( 903) hydrogen bonds : angle 5.39529 ( 2709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 482 time to evaluate : 0.457 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: B 32 ILE cc_start: 0.9052 (mm) cc_final: 0.8598 (mt) REVERT: C 3 GLU cc_start: 0.8810 (mp0) cc_final: 0.8472 (mm-30) REVERT: D 3 GLU cc_start: 0.8599 (mp0) cc_final: 0.8323 (mp0) REVERT: D 10 ARG cc_start: 0.8686 (mmp80) cc_final: 0.7701 (mmp80) REVERT: D 29 LYS cc_start: 0.9333 (mmpt) cc_final: 0.9130 (mmmt) REVERT: G 29 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9123 (mmtp) REVERT: J 24 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8706 (mm-30) REVERT: N 29 LYS cc_start: 0.9408 (mmpt) cc_final: 0.9179 (mmmt) REVERT: O 22 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8526 (ptpt) REVERT: Q 29 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9103 (mmtp) REVERT: R 12 LEU cc_start: 0.9617 (tp) cc_final: 0.9313 (tp) REVERT: S 3 GLU cc_start: 0.8558 (mp0) cc_final: 0.8249 (mm-30) REVERT: T 3 GLU cc_start: 0.8760 (mp0) cc_final: 0.8365 (mm-30) REVERT: T 29 LYS cc_start: 0.9349 (mmmt) cc_final: 0.9054 (mmmt) REVERT: T 36 GLN cc_start: 0.8331 (tt0) cc_final: 0.7882 (tt0) REVERT: b 3 GLU cc_start: 0.8711 (mp0) cc_final: 0.8335 (mp0) REVERT: e 3 GLU cc_start: 0.8800 (mp0) cc_final: 0.8376 (mm-30) REVERT: f 3 GLU cc_start: 0.8739 (mp0) cc_final: 0.8309 (mm-30) REVERT: h 27 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8781 (pttp) REVERT: j 5 LEU cc_start: 0.9332 (mt) cc_final: 0.9097 (mm) REVERT: j 29 LYS cc_start: 0.9248 (tptt) cc_final: 0.8714 (tmmt) REVERT: l 3 GLU cc_start: 0.8716 (mp0) cc_final: 0.8234 (mp0) REVERT: l 19 LEU cc_start: 0.9172 (mt) cc_final: 0.8558 (tt) REVERT: l 29 LYS cc_start: 0.9280 (tptt) cc_final: 0.8873 (tmmt) REVERT: n 29 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8777 (tmmt) outliers start: 4 outliers final: 1 residues processed: 484 average time/residue: 0.1963 time to fit residues: 116.7212 Evaluate side-chains 382 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.094645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.085121 restraints weight = 62316.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.086440 restraints weight = 35744.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.087329 restraints weight = 23877.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.087953 restraints weight = 17282.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.088365 restraints weight = 13415.196| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.8405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11439 Z= 0.178 Angle : 0.859 7.843 15211 Z= 0.459 Chirality : 0.039 0.182 1927 Planarity : 0.003 0.034 1886 Dihedral : 5.672 70.424 1558 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1394 helix: 0.69 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 10 Details of bonding type rmsd covalent geometry : bond 0.00406 (11439) covalent geometry : angle 0.85893 (15211) hydrogen bonds : bond 0.03941 ( 903) hydrogen bonds : angle 5.48655 ( 2709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 0.511 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: B 32 ILE cc_start: 0.9047 (mm) cc_final: 0.8640 (mt) REVERT: D 3 GLU cc_start: 0.8503 (mp0) cc_final: 0.8287 (mp0) REVERT: G 29 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8887 (mmmt) REVERT: J 24 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8632 (mm-30) REVERT: M 24 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8608 (mm-30) REVERT: N 31 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8162 (mp0) REVERT: O 22 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8499 (ptpt) REVERT: P 3 GLU cc_start: 0.8661 (mp0) cc_final: 0.8369 (mp0) REVERT: Q 29 LYS cc_start: 0.9320 (mmmt) cc_final: 0.9041 (mmtp) REVERT: S 3 GLU cc_start: 0.8467 (mp0) cc_final: 0.8187 (mm-30) REVERT: T 29 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9084 (mmmt) REVERT: X 29 LYS cc_start: 0.9322 (mmmm) cc_final: 0.9106 (mmtm) REVERT: b 3 GLU cc_start: 0.8674 (mp0) cc_final: 0.8269 (mp0) REVERT: d 36 GLN cc_start: 0.8053 (tt0) cc_final: 0.7493 (tt0) REVERT: e 3 GLU cc_start: 0.8730 (mp0) cc_final: 0.8403 (mm-30) REVERT: f 3 GLU cc_start: 0.8603 (mp0) cc_final: 0.8381 (mm-30) REVERT: i 24 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8570 (mm-30) REVERT: i 29 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8689 (mmmt) REVERT: j 5 LEU cc_start: 0.9333 (mt) cc_final: 0.9077 (mm) REVERT: j 29 LYS cc_start: 0.9134 (tptt) cc_final: 0.8649 (tmmt) REVERT: l 3 GLU cc_start: 0.8518 (mp0) cc_final: 0.8228 (mp0) REVERT: l 13 GLU cc_start: 0.9165 (pp20) cc_final: 0.8759 (pp20) REVERT: l 17 GLU cc_start: 0.9030 (mp0) cc_final: 0.8730 (mp0) REVERT: l 19 LEU cc_start: 0.9209 (mt) cc_final: 0.8578 (tt) REVERT: l 29 LYS cc_start: 0.9200 (tptt) cc_final: 0.8903 (tmmt) REVERT: n 29 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8797 (tmmt) REVERT: o 26 LEU cc_start: 0.9137 (mt) cc_final: 0.8928 (tp) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.1873 time to fit residues: 110.2643 Evaluate side-chains 387 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.092265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.082831 restraints weight = 63381.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.084141 restraints weight = 36642.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.084999 restraints weight = 24192.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.085616 restraints weight = 17793.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.086079 restraints weight = 13904.056| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.8561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11439 Z= 0.208 Angle : 0.937 8.811 15211 Z= 0.499 Chirality : 0.042 0.195 1927 Planarity : 0.004 0.068 1886 Dihedral : 5.876 76.694 1558 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1394 helix: 0.51 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 6 Details of bonding type rmsd covalent geometry : bond 0.00470 (11439) covalent geometry : angle 0.93693 (15211) hydrogen bonds : bond 0.04210 ( 903) hydrogen bonds : angle 5.76910 ( 2709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 455 time to evaluate : 0.513 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: B 32 ILE cc_start: 0.9133 (mm) cc_final: 0.8713 (mt) REVERT: G 29 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8847 (mmmt) REVERT: H 29 LYS cc_start: 0.9391 (tppt) cc_final: 0.9174 (mmmt) REVERT: J 24 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8696 (mm-30) REVERT: M 24 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8674 (mm-30) REVERT: O 22 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8558 (ptpp) REVERT: P 3 GLU cc_start: 0.8665 (mp0) cc_final: 0.8428 (mp0) REVERT: Q 29 LYS cc_start: 0.9300 (mmmt) cc_final: 0.9084 (mmtp) REVERT: R 12 LEU cc_start: 0.9595 (tp) cc_final: 0.9350 (tp) REVERT: S 3 GLU cc_start: 0.8390 (mp0) cc_final: 0.8165 (mm-30) REVERT: U 29 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8966 (mmmt) REVERT: X 29 LYS cc_start: 0.9358 (mmmm) cc_final: 0.9139 (mmtm) REVERT: a 32 ILE cc_start: 0.9161 (mt) cc_final: 0.8855 (tp) REVERT: b 3 GLU cc_start: 0.8599 (mp0) cc_final: 0.8206 (mp0) REVERT: e 3 GLU cc_start: 0.8659 (mp0) cc_final: 0.8331 (mm-30) REVERT: f 3 GLU cc_start: 0.8563 (mp0) cc_final: 0.8357 (mm-30) REVERT: h 22 LYS cc_start: 0.9375 (ptpp) cc_final: 0.8964 (ptpp) REVERT: j 5 LEU cc_start: 0.9364 (mt) cc_final: 0.9061 (mm) REVERT: j 29 LYS cc_start: 0.9117 (tptt) cc_final: 0.8649 (tmmt) REVERT: l 3 GLU cc_start: 0.8633 (mp0) cc_final: 0.8349 (mm-30) REVERT: l 13 GLU cc_start: 0.9172 (pp20) cc_final: 0.8708 (pp20) REVERT: l 17 GLU cc_start: 0.9053 (mp0) cc_final: 0.8789 (mp0) REVERT: l 19 LEU cc_start: 0.9251 (mt) cc_final: 0.8600 (tt) REVERT: l 29 LYS cc_start: 0.9152 (tptt) cc_final: 0.8873 (tmmt) REVERT: n 29 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8904 (tmmt) outliers start: 2 outliers final: 0 residues processed: 456 average time/residue: 0.1821 time to fit residues: 102.7668 Evaluate side-chains 375 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 0.0060 chunk 76 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 118 optimal weight: 0.1980 chunk 7 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 overall best weight: 3.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.094717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085281 restraints weight = 62546.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.086571 restraints weight = 36549.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087479 restraints weight = 24520.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.088103 restraints weight = 17967.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.088509 restraints weight = 14023.032| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.8678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11439 Z= 0.190 Angle : 0.891 8.360 15211 Z= 0.472 Chirality : 0.041 0.204 1927 Planarity : 0.003 0.039 1886 Dihedral : 5.909 75.261 1558 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.18 % Allowed : 1.17 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1394 helix: 0.61 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 6 Details of bonding type rmsd covalent geometry : bond 0.00434 (11439) covalent geometry : angle 0.89125 (15211) hydrogen bonds : bond 0.04019 ( 903) hydrogen bonds : angle 5.65706 ( 2709) =============================================================================== Job complete usr+sys time: 2314.34 seconds wall clock time: 40 minutes 46.35 seconds (2446.35 seconds total)