Starting phenix.real_space_refine on Tue Jul 29 05:37:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wl0_21814/07_2025/6wl0_21814.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wl0_21814/07_2025/6wl0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wl0_21814/07_2025/6wl0_21814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wl0_21814/07_2025/6wl0_21814.map" model { file = "/net/cci-nas-00/data/ceres_data/6wl0_21814/07_2025/6wl0_21814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wl0_21814/07_2025/6wl0_21814.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, i, h, k, j, m, l, o, n Time building chain proxies: 2.69, per 1000 atoms: 0.23 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: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.75 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: 3.25 Time building geometry restraints manager: 3.11 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'o' selection = chain 'n' } 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: 222.510 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 23.360 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.48 (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 hydrogen bonds : bond 0.29478 ( 903) hydrogen bonds : angle 9.10174 ( 2709) covalent geometry : bond 0.00593 (11439) covalent geometry : angle 0.82178 (15211) *********************** 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 : 1.271 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: 0.8751 (tpm170) cc_final: 0.8266 (tpm170) REVERT: A 32 ILE cc_start: 0.9162 (mt) cc_final: 0.8800 (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: 0.8991 (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: 0.8231 (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: 0.9316 (mm-30) cc_final: 0.8909 (mm-30) REVERT: K 10 ARG cc_start: 0.8808 (tpm170) cc_final: 0.7828 (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: 0.7770 (tpm170) REVERT: R 36 GLN cc_start: 0.7781 (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: 0.8652 (tpm170) cc_final: 0.8244 (tpm170) REVERT: Z 36 GLN cc_start: 0.8594 (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: 0.9326 (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: 0.9096 (mt) cc_final: 0.8763 (tp) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.4060 time to fit residues: 337.7916 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 : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.063666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055091 restraints weight = 53216.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056341 restraints weight = 36781.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.057319 restraints weight = 27819.381| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4949 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= 0.189 Angle : 0.674 6.681 15211 Z= 0.367 Chirality : 0.034 0.131 1927 Planarity : 0.004 0.029 1886 Dihedral : 6.718 32.750 1558 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.45 % Allowed : 10.48 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.21), residues: 1394 helix: -1.25 (0.13), 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 C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 903) hydrogen bonds : angle 5.41152 ( 2709) covalent geometry : bond 0.00398 (11439) covalent geometry : angle 0.67387 (15211) *********************** 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 574 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 569 time to evaluate : 1.463 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: A 3 GLU cc_start: 0.8505 (mp0) cc_final: 0.8183 (mm-30) REVERT: D 3 GLU cc_start: 0.8715 (mp0) cc_final: 0.8426 (mm-30) REVERT: E 29 LYS cc_start: 0.9436 (mmpt) cc_final: 0.9128 (mmmt) REVERT: E 31 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8376 (mm-30) REVERT: G 3 GLU cc_start: 0.8850 (mp0) cc_final: 0.8458 (mp0) REVERT: I 29 LYS cc_start: 0.9441 (mmpt) cc_final: 0.9199 (mmmt) REVERT: I 32 ILE cc_start: 0.9195 (mm) cc_final: 0.8693 (mt) REVERT: J 3 GLU cc_start: 0.8490 (mp0) cc_final: 0.8128 (mp0) REVERT: J 29 LYS cc_start: 0.9418 (mmtt) cc_final: 0.9148 (mmmt) REVERT: M 3 GLU cc_start: 0.8578 (mp0) cc_final: 0.8231 (tp30) REVERT: O 31 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8495 (mm-30) REVERT: P 3 GLU cc_start: 0.8327 (mp0) cc_final: 0.7626 (mp0) REVERT: R 12 LEU cc_start: 0.9538 (tt) cc_final: 0.9151 (tp) REVERT: R 24 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8974 (mm-30) REVERT: U 29 LYS cc_start: 0.9282 (mmpt) cc_final: 0.8935 (tppt) REVERT: V 12 LEU cc_start: 0.9681 (mt) cc_final: 0.8907 (mt) REVERT: V 36 GLN cc_start: 0.8398 (mt0) cc_final: 0.7949 (tt0) REVERT: Y 3 GLU cc_start: 0.8444 (mp0) cc_final: 0.8237 (mm-30) REVERT: d 3 GLU cc_start: 0.8800 (mp0) cc_final: 0.8332 (mm-30) REVERT: e 27 LYS cc_start: 0.9496 (tmmt) cc_final: 0.9294 (ttpp) REVERT: f 10 ARG cc_start: 0.8612 (mmp80) cc_final: 0.8378 (mmp80) REVERT: f 29 LYS cc_start: 0.9481 (tppt) cc_final: 0.9225 (mmmt) REVERT: j 3 GLU cc_start: 0.8883 (mp0) cc_final: 0.8162 (mp0) REVERT: j 5 LEU cc_start: 0.9317 (mt) cc_final: 0.9110 (mm) REVERT: j 29 LYS cc_start: 0.9380 (tptt) cc_final: 0.8951 (tmmt) REVERT: k 24 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8928 (mm-30) REVERT: l 19 LEU cc_start: 0.9311 (mt) cc_final: 0.8716 (tp) REVERT: l 29 LYS cc_start: 0.9311 (tptt) cc_final: 0.8980 (tmmt) REVERT: m 5 LEU cc_start: 0.9462 (mt) cc_final: 0.9262 (mm) REVERT: n 29 LYS cc_start: 0.9360 (mmtt) cc_final: 0.8981 (tmmt) REVERT: o 24 GLU cc_start: 0.9501 (mm-30) cc_final: 0.8806 (mm-30) outliers start: 5 outliers final: 0 residues processed: 569 average time/residue: 0.4039 time to fit residues: 283.2951 Evaluate side-chains 419 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.090589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081808 restraints weight = 63187.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.083139 restraints weight = 35028.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.083989 restraints weight = 22560.393| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11439 Z= 0.185 Angle : 0.662 9.403 15211 Z= 0.354 Chirality : 0.035 0.134 1927 Planarity : 0.005 0.086 1886 Dihedral : 5.567 32.346 1558 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.45 % Allowed : 6.50 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1394 helix: -0.36 (0.13), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 10 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 903) hydrogen bonds : angle 5.17718 ( 2709) covalent geometry : bond 0.00395 (11439) covalent geometry : angle 0.66184 (15211) *********************** 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 561 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 556 time to evaluate : 1.287 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: A 3 GLU cc_start: 0.8527 (mp0) cc_final: 0.8269 (mm-30) REVERT: B 36 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5588 (pp30) REVERT: C 3 GLU cc_start: 0.8739 (mp0) cc_final: 0.8488 (mm-30) REVERT: C 10 ARG cc_start: 0.8608 (mmp80) cc_final: 0.8394 (mmp80) REVERT: D 3 GLU cc_start: 0.8799 (mp0) cc_final: 0.8518 (mm-30) REVERT: G 3 GLU cc_start: 0.8750 (mp0) cc_final: 0.8485 (mm-30) REVERT: H 36 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.5952 (pp30) REVERT: I 32 ILE cc_start: 0.9095 (mm) cc_final: 0.8866 (mt) REVERT: L 3 GLU cc_start: 0.8820 (mp0) cc_final: 0.8554 (mm-30) REVERT: L 29 LYS cc_start: 0.9289 (mmtt) cc_final: 0.9080 (mmmt) REVERT: L 36 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5715 (pp30) REVERT: N 29 LYS cc_start: 0.9241 (mmmt) cc_final: 0.9035 (mmmt) REVERT: P 36 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6153 (pp30) REVERT: Q 29 LYS cc_start: 0.9368 (mmpt) cc_final: 0.9166 (mmmt) REVERT: T 3 GLU cc_start: 0.8597 (mp0) cc_final: 0.8368 (mm-30) REVERT: V 8 GLU cc_start: 0.8932 (tp30) cc_final: 0.8596 (tp30) REVERT: V 12 LEU cc_start: 0.9542 (mt) cc_final: 0.9051 (mt) REVERT: V 13 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8087 (tm-30) REVERT: X 36 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5810 (pp30) REVERT: Y 3 GLU cc_start: 0.8443 (mp0) cc_final: 0.8175 (tp30) REVERT: Z 5 LEU cc_start: 0.9396 (mm) cc_final: 0.9180 (mm) REVERT: a 3 GLU cc_start: 0.8466 (mp0) cc_final: 0.8223 (mm-30) REVERT: d 3 GLU cc_start: 0.8735 (mp0) cc_final: 0.8242 (mp0) REVERT: j 5 LEU cc_start: 0.9380 (mt) cc_final: 0.9005 (mm) REVERT: j 29 LYS cc_start: 0.9273 (tptt) cc_final: 0.8921 (tmmt) REVERT: l 3 GLU cc_start: 0.8498 (mp0) cc_final: 0.8264 (mp0) REVERT: l 19 LEU cc_start: 0.9289 (mt) cc_final: 0.8711 (tp) REVERT: l 29 LYS cc_start: 0.9248 (tptt) cc_final: 0.8942 (tmmt) REVERT: m 5 LEU cc_start: 0.9478 (mt) cc_final: 0.9221 (mm) REVERT: m 13 GLU cc_start: 0.9042 (pp20) cc_final: 0.8813 (pp20) REVERT: n 29 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8907 (tmmt) outliers start: 5 outliers final: 0 residues processed: 556 average time/residue: 0.4143 time to fit residues: 282.2264 Evaluate side-chains 421 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 416 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055285 restraints weight = 51900.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056626 restraints weight = 35857.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.057554 restraints weight = 26928.858| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.7033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11439 Z= 0.220 Angle : 0.732 10.882 15211 Z= 0.389 Chirality : 0.038 0.150 1927 Planarity : 0.004 0.054 1886 Dihedral : 5.870 66.727 1558 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1394 helix: -0.12 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 6 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 903) hydrogen bonds : angle 5.45769 ( 2709) covalent geometry : bond 0.00463 (11439) covalent geometry : angle 0.73182 (15211) *********************** 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 512 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 511 time to evaluate : 1.281 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: A 3 GLU cc_start: 0.8862 (mp0) cc_final: 0.8497 (mm-30) REVERT: A 29 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9075 (mmmt) REVERT: B 29 LYS cc_start: 0.9457 (mmpt) cc_final: 0.9038 (mmmt) REVERT: B 36 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6375 (pp30) REVERT: C 3 GLU cc_start: 0.8909 (mp0) cc_final: 0.8517 (mm-30) REVERT: D 3 GLU cc_start: 0.8652 (mp0) cc_final: 0.8346 (mm-30) REVERT: F 29 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9073 (mmmt) REVERT: G 29 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9111 (mmmt) REVERT: I 29 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9015 (mmmt) REVERT: K 3 GLU cc_start: 0.8705 (mp0) cc_final: 0.8479 (mp0) REVERT: L 32 ILE cc_start: 0.8835 (mt) cc_final: 0.8508 (mt) REVERT: M 3 GLU cc_start: 0.8730 (mp0) cc_final: 0.8335 (mm-30) REVERT: N 8 GLU cc_start: 0.9078 (mp0) cc_final: 0.8845 (mp0) REVERT: N 29 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9236 (mmmt) REVERT: P 3 GLU cc_start: 0.8936 (mp0) cc_final: 0.8118 (mp0) REVERT: Q 29 LYS cc_start: 0.9455 (mmpt) cc_final: 0.9231 (mmmt) REVERT: R 34 LYS cc_start: 0.8859 (tppt) cc_final: 0.8319 (tppt) REVERT: S 3 GLU cc_start: 0.8643 (mp0) cc_final: 0.8320 (tp30) REVERT: S 29 LYS cc_start: 0.9454 (mmmt) cc_final: 0.9140 (mmmt) REVERT: U 10 ARG cc_start: 0.8927 (mmm160) cc_final: 0.8310 (mmm160) REVERT: U 34 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8473 (tppt) REVERT: V 8 GLU cc_start: 0.9123 (tp30) cc_final: 0.8787 (tp30) REVERT: V 12 LEU cc_start: 0.9531 (mt) cc_final: 0.8963 (mt) REVERT: Y 3 GLU cc_start: 0.8739 (mp0) cc_final: 0.8306 (tp30) REVERT: Y 10 ARG cc_start: 0.8806 (mmp80) cc_final: 0.8600 (mmp80) REVERT: a 3 GLU cc_start: 0.8823 (mp0) cc_final: 0.8536 (mm-30) REVERT: e 3 GLU cc_start: 0.8915 (mp0) cc_final: 0.8398 (mm-30) REVERT: e 33 LEU cc_start: 0.7539 (mt) cc_final: 0.7294 (mt) REVERT: j 5 LEU cc_start: 0.9346 (mt) cc_final: 0.9069 (mm) REVERT: j 29 LYS cc_start: 0.9381 (tptt) cc_final: 0.8959 (tmmt) REVERT: l 3 GLU cc_start: 0.8780 (mp0) cc_final: 0.8471 (mm-30) REVERT: l 19 LEU cc_start: 0.9268 (mt) cc_final: 0.8731 (tt) REVERT: l 29 LYS cc_start: 0.9394 (tptt) cc_final: 0.9011 (tmmt) REVERT: n 29 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8954 (pttp) outliers start: 1 outliers final: 0 residues processed: 511 average time/residue: 0.4124 time to fit residues: 258.2827 Evaluate side-chains 385 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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** X 36 GLN Y 36 GLN b 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.092523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.083499 restraints weight = 63250.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.084766 restraints weight = 35039.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.085603 restraints weight = 22850.185| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11439 Z= 0.159 Angle : 0.656 8.191 15211 Z= 0.352 Chirality : 0.035 0.156 1927 Planarity : 0.004 0.066 1886 Dihedral : 6.072 76.527 1558 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 0.27 % Allowed : 3.52 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1394 helix: 0.55 (0.12), 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 X 10 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 903) hydrogen bonds : angle 5.03552 ( 2709) covalent geometry : bond 0.00347 (11439) covalent geometry : angle 0.65558 (15211) *********************** 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 527 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 524 time to evaluate : 1.335 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: A 3 GLU cc_start: 0.8709 (mp0) cc_final: 0.8310 (mm-30) REVERT: B 32 ILE cc_start: 0.9221 (mt) cc_final: 0.8758 (mt) REVERT: C 3 GLU cc_start: 0.8852 (mp0) cc_final: 0.8588 (mp0) REVERT: C 10 ARG cc_start: 0.8928 (mmp80) cc_final: 0.8498 (mmp-170) REVERT: D 3 GLU cc_start: 0.8718 (mp0) cc_final: 0.8458 (mm-30) REVERT: F 29 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9116 (mmmt) REVERT: G 29 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9049 (mmmt) REVERT: I 29 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9059 (mmmt) REVERT: J 24 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8811 (mm-30) REVERT: K 3 GLU cc_start: 0.8536 (mp0) cc_final: 0.8312 (mp0) REVERT: M 3 GLU cc_start: 0.8732 (mp0) cc_final: 0.8308 (mm-30) REVERT: O 31 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8522 (mp0) REVERT: P 3 GLU cc_start: 0.8906 (mp0) cc_final: 0.8352 (mm-30) REVERT: S 3 GLU cc_start: 0.8621 (mp0) cc_final: 0.8284 (mm-30) REVERT: U 10 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8127 (mmm160) REVERT: V 8 GLU cc_start: 0.9006 (tp30) cc_final: 0.8627 (tp30) REVERT: V 12 LEU cc_start: 0.9586 (mt) cc_final: 0.8906 (mt) REVERT: X 29 LYS cc_start: 0.9422 (mmmt) cc_final: 0.9138 (mmtm) REVERT: Y 3 GLU cc_start: 0.8806 (mp0) cc_final: 0.8365 (mm-30) REVERT: a 3 GLU cc_start: 0.8699 (mp0) cc_final: 0.8454 (mm-30) REVERT: b 3 GLU cc_start: 0.8822 (mp0) cc_final: 0.8402 (mp0) REVERT: c 29 LYS cc_start: 0.9345 (mmmt) cc_final: 0.9095 (mmmt) REVERT: e 3 GLU cc_start: 0.8905 (mp0) cc_final: 0.8338 (mm-30) REVERT: f 29 LYS cc_start: 0.9339 (mmmt) cc_final: 0.9087 (mmmt) REVERT: j 5 LEU cc_start: 0.9358 (mt) cc_final: 0.9092 (mm) REVERT: j 29 LYS cc_start: 0.9304 (tptt) cc_final: 0.8933 (tmmt) REVERT: l 19 LEU cc_start: 0.9246 (mt) cc_final: 0.8563 (tp) REVERT: l 29 LYS cc_start: 0.9317 (tptt) cc_final: 0.8942 (tmmt) REVERT: n 29 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8851 (tmmt) outliers start: 3 outliers final: 0 residues processed: 525 average time/residue: 0.4115 time to fit residues: 264.4612 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 : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.053340 restraints weight = 54369.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054668 restraints weight = 37200.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055610 restraints weight = 27762.006| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.7640 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= 0.248 Angle : 0.819 10.626 15211 Z= 0.433 Chirality : 0.040 0.172 1927 Planarity : 0.005 0.061 1886 Dihedral : 6.568 76.662 1558 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1394 helix: 0.30 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 903) hydrogen bonds : angle 5.76649 ( 2709) covalent geometry : bond 0.00523 (11439) covalent geometry : angle 0.81897 (15211) *********************** 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 461 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.398 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: A 3 GLU cc_start: 0.8806 (mp0) cc_final: 0.8416 (mp0) REVERT: A 29 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9049 (mmmt) REVERT: B 29 LYS cc_start: 0.9500 (mmmt) cc_final: 0.9215 (mmmt) REVERT: C 3 GLU cc_start: 0.8969 (mp0) cc_final: 0.8720 (mp0) REVERT: D 3 GLU cc_start: 0.8633 (mp0) cc_final: 0.8417 (mm-30) REVERT: F 29 LYS cc_start: 0.9477 (mmmt) cc_final: 0.9113 (mmmt) REVERT: F 31 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8883 (mm-30) REVERT: G 29 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9119 (mmmt) REVERT: I 13 GLU cc_start: 0.9323 (pp20) cc_final: 0.9117 (pp20) REVERT: J 24 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9076 (mm-30) REVERT: K 29 LYS cc_start: 0.9482 (mmmt) cc_final: 0.9220 (mmmt) REVERT: M 3 GLU cc_start: 0.8740 (mp0) cc_final: 0.8390 (tp30) REVERT: N 8 GLU cc_start: 0.9064 (mp0) cc_final: 0.8837 (mp0) REVERT: N 29 LYS cc_start: 0.9426 (mmmt) cc_final: 0.9188 (mmmt) REVERT: P 3 GLU cc_start: 0.9000 (mp0) cc_final: 0.8467 (mm-30) REVERT: S 3 GLU cc_start: 0.8710 (mp0) cc_final: 0.8450 (mm-30) REVERT: U 17 GLU cc_start: 0.8993 (mp0) cc_final: 0.8704 (mp0) REVERT: U 19 LEU cc_start: 0.9299 (mp) cc_final: 0.8986 (mp) REVERT: U 22 LYS cc_start: 0.9231 (mtmm) cc_final: 0.8836 (mttt) REVERT: V 8 GLU cc_start: 0.9111 (tp30) cc_final: 0.8600 (tp30) REVERT: V 12 LEU cc_start: 0.9565 (mt) cc_final: 0.8504 (mt) REVERT: X 36 GLN cc_start: 0.8140 (pt0) cc_final: 0.7894 (pp30) REVERT: Y 3 GLU cc_start: 0.8795 (mp0) cc_final: 0.8318 (mm-30) REVERT: Z 10 ARG cc_start: 0.8994 (mmm-85) cc_final: 0.8681 (mmm-85) REVERT: a 3 GLU cc_start: 0.8875 (mp0) cc_final: 0.8624 (mm-30) REVERT: b 3 GLU cc_start: 0.8807 (mp0) cc_final: 0.8298 (mp0) REVERT: b 10 ARG cc_start: 0.8397 (mmp80) cc_final: 0.8036 (mmp80) REVERT: e 3 GLU cc_start: 0.8870 (mp0) cc_final: 0.8345 (mm-30) REVERT: f 29 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9257 (mmmt) REVERT: j 5 LEU cc_start: 0.9341 (mt) cc_final: 0.9057 (mm) REVERT: j 8 GLU cc_start: 0.8617 (pp20) cc_final: 0.8379 (pp20) REVERT: j 29 LYS cc_start: 0.9329 (tptt) cc_final: 0.8684 (tmmt) REVERT: l 19 LEU cc_start: 0.9227 (mt) cc_final: 0.8656 (tt) REVERT: l 29 LYS cc_start: 0.9394 (tptt) cc_final: 0.8995 (tmmt) REVERT: m 31 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8814 (tp30) REVERT: n 29 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8868 (tmmt) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.4127 time to fit residues: 232.4937 Evaluate side-chains 356 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056857 restraints weight = 53735.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058278 restraints weight = 36698.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059287 restraints weight = 27241.766| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.7941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11439 Z= 0.172 Angle : 0.732 7.937 15211 Z= 0.393 Chirality : 0.038 0.305 1927 Planarity : 0.003 0.049 1886 Dihedral : 6.233 75.349 1558 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.09 % Allowed : 2.62 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1394 helix: 0.66 (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 X 10 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 903) hydrogen bonds : angle 5.38795 ( 2709) covalent geometry : bond 0.00386 (11439) covalent geometry : angle 0.73170 (15211) *********************** 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 486 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 1.425 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: A 3 GLU cc_start: 0.8754 (mp0) cc_final: 0.8340 (mp0) REVERT: B 29 LYS cc_start: 0.9469 (mmmt) cc_final: 0.9151 (mmmt) REVERT: C 3 GLU cc_start: 0.8937 (mp0) cc_final: 0.8649 (mp0) REVERT: D 3 GLU cc_start: 0.8660 (mp0) cc_final: 0.8427 (mm-30) REVERT: D 29 LYS cc_start: 0.9329 (mmpt) cc_final: 0.9109 (mmmt) REVERT: F 29 LYS cc_start: 0.9468 (mmmt) cc_final: 0.9105 (mmmt) REVERT: G 24 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8555 (mm-30) REVERT: G 29 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9178 (mmmt) REVERT: J 24 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8924 (mm-30) REVERT: K 3 GLU cc_start: 0.8587 (mp0) cc_final: 0.8172 (mp0) REVERT: M 3 GLU cc_start: 0.8643 (mp0) cc_final: 0.8356 (mp0) REVERT: N 8 GLU cc_start: 0.9074 (mp0) cc_final: 0.8846 (mp0) REVERT: N 29 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9181 (mmmt) REVERT: N 31 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8438 (mp0) REVERT: O 29 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9280 (mmmt) REVERT: P 3 GLU cc_start: 0.8812 (mp0) cc_final: 0.8386 (mm-30) REVERT: Q 29 LYS cc_start: 0.9432 (mmpt) cc_final: 0.9194 (mmmt) REVERT: S 3 GLU cc_start: 0.8616 (mp0) cc_final: 0.8247 (mm-30) REVERT: V 8 GLU cc_start: 0.9114 (tp30) cc_final: 0.8608 (tp30) REVERT: V 12 LEU cc_start: 0.9606 (mt) cc_final: 0.8542 (mt) REVERT: V 34 LYS cc_start: 0.9300 (tppt) cc_final: 0.8965 (tppp) REVERT: W 24 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8311 (mm-30) REVERT: X 36 GLN cc_start: 0.8130 (pt0) cc_final: 0.7871 (pp30) REVERT: Y 3 GLU cc_start: 0.8795 (mp0) cc_final: 0.8403 (mm-30) REVERT: Z 10 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8548 (mmm-85) REVERT: Z 29 LYS cc_start: 0.9352 (mmpt) cc_final: 0.9108 (mmmt) REVERT: a 3 GLU cc_start: 0.8867 (mp0) cc_final: 0.8620 (mm-30) REVERT: e 3 GLU cc_start: 0.8813 (mp0) cc_final: 0.8357 (mm-30) REVERT: j 5 LEU cc_start: 0.9361 (mt) cc_final: 0.9105 (mm) REVERT: j 29 LYS cc_start: 0.9316 (tptt) cc_final: 0.8727 (tmmt) REVERT: l 10 ARG cc_start: 0.8451 (ttt180) cc_final: 0.7771 (ttt180) REVERT: l 19 LEU cc_start: 0.9186 (mt) cc_final: 0.8525 (tt) REVERT: l 29 LYS cc_start: 0.9390 (tptt) cc_final: 0.8998 (tmmt) REVERT: n 29 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8829 (tmmt) outliers start: 1 outliers final: 0 residues processed: 485 average time/residue: 0.4218 time to fit residues: 249.5329 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 : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.066296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.057280 restraints weight = 52444.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058581 restraints weight = 36957.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059539 restraints weight = 28167.722| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.8198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11439 Z= 0.184 Angle : 0.797 8.059 15211 Z= 0.431 Chirality : 0.038 0.166 1927 Planarity : 0.004 0.038 1886 Dihedral : 6.522 75.235 1558 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (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 0.006 0.001 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 903) hydrogen bonds : angle 5.60794 ( 2709) covalent geometry : bond 0.00412 (11439) covalent geometry : angle 0.79652 (15211) *********************** 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 477 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 1.412 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: A 3 GLU cc_start: 0.8756 (mp0) cc_final: 0.8378 (mp0) REVERT: B 29 LYS cc_start: 0.9455 (mmmt) cc_final: 0.9162 (mmmt) REVERT: C 3 GLU cc_start: 0.8866 (mp0) cc_final: 0.8604 (mp0) REVERT: D 3 GLU cc_start: 0.8647 (mp0) cc_final: 0.8431 (mm-30) REVERT: E 24 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8531 (mm-30) REVERT: F 29 LYS cc_start: 0.9390 (mmmt) cc_final: 0.9147 (mmmt) REVERT: J 24 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8854 (mm-30) REVERT: M 3 GLU cc_start: 0.8669 (mp0) cc_final: 0.8223 (mm-30) REVERT: M 34 LYS cc_start: 0.9460 (ttpp) cc_final: 0.9047 (tptp) REVERT: N 8 GLU cc_start: 0.9100 (mp0) cc_final: 0.8831 (mp0) REVERT: N 29 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9211 (mmmt) REVERT: P 3 GLU cc_start: 0.8832 (mp0) cc_final: 0.8460 (mm-30) REVERT: S 3 GLU cc_start: 0.8532 (mp0) cc_final: 0.8229 (mm-30) REVERT: S 24 GLU cc_start: 0.8697 (mp0) cc_final: 0.8375 (mp0) REVERT: U 19 LEU cc_start: 0.9296 (mp) cc_final: 0.9012 (mp) REVERT: U 22 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8603 (ptpt) REVERT: U 29 LYS cc_start: 0.9268 (mmmt) cc_final: 0.9032 (mmmt) REVERT: V 8 GLU cc_start: 0.8999 (tp30) cc_final: 0.8498 (tp30) REVERT: V 12 LEU cc_start: 0.9570 (mt) cc_final: 0.8522 (mt) REVERT: X 31 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8472 (mt-10) REVERT: X 36 GLN cc_start: 0.8055 (pt0) cc_final: 0.7798 (pp30) REVERT: Y 3 GLU cc_start: 0.8892 (mp0) cc_final: 0.8534 (mm-30) REVERT: Z 29 LYS cc_start: 0.9353 (mmpt) cc_final: 0.9121 (mmmt) REVERT: a 3 GLU cc_start: 0.8872 (mp0) cc_final: 0.8545 (mm-30) REVERT: e 3 GLU cc_start: 0.8859 (mp0) cc_final: 0.8409 (mm-30) REVERT: j 5 LEU cc_start: 0.9337 (mt) cc_final: 0.9067 (mm) REVERT: j 19 LEU cc_start: 0.9245 (mt) cc_final: 0.8788 (tt) REVERT: j 29 LYS cc_start: 0.9303 (tptt) cc_final: 0.8747 (tmmt) REVERT: l 19 LEU cc_start: 0.9225 (mt) cc_final: 0.8568 (tt) REVERT: l 29 LYS cc_start: 0.9407 (mmmt) cc_final: 0.8934 (tmmt) REVERT: n 29 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8868 (tmmt) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.4184 time to fit residues: 243.6205 Evaluate side-chains 376 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** i 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 = 0.3436 r_free = 0.3436 target = 0.065929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057054 restraints weight = 52919.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058412 restraints weight = 36722.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059400 restraints weight = 27587.868| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.8362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11439 Z= 0.197 Angle : 0.872 10.530 15211 Z= 0.466 Chirality : 0.040 0.225 1927 Planarity : 0.004 0.034 1886 Dihedral : 6.339 69.908 1558 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.18 % Allowed : 1.72 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1394 helix: 0.45 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 6 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 903) hydrogen bonds : angle 5.74633 ( 2709) covalent geometry : bond 0.00448 (11439) covalent geometry : angle 0.87205 (15211) *********************** 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 473 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 471 time to evaluate : 1.300 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: A 3 GLU cc_start: 0.8761 (mp0) cc_final: 0.8397 (mp0) REVERT: B 29 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9169 (mmmt) REVERT: C 3 GLU cc_start: 0.8858 (mp0) cc_final: 0.8595 (mp0) REVERT: D 29 LYS cc_start: 0.9274 (mmpt) cc_final: 0.9055 (mmmt) REVERT: G 29 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9195 (mmmt) REVERT: J 22 LYS cc_start: 0.9373 (ptpp) cc_final: 0.8938 (ptpp) REVERT: J 24 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8968 (mm-30) REVERT: M 3 GLU cc_start: 0.8771 (mp0) cc_final: 0.8397 (mm-30) REVERT: M 24 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8751 (mm-30) REVERT: M 34 LYS cc_start: 0.9462 (ttpp) cc_final: 0.9028 (tptp) REVERT: N 29 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9198 (mmmt) REVERT: O 29 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9305 (mmmt) REVERT: P 3 GLU cc_start: 0.8792 (mp0) cc_final: 0.8459 (mm-30) REVERT: S 3 GLU cc_start: 0.8516 (mp0) cc_final: 0.8221 (mm-30) REVERT: S 20 LYS cc_start: 0.9700 (ttmt) cc_final: 0.9475 (ttmm) REVERT: V 8 GLU cc_start: 0.9063 (tp30) cc_final: 0.8536 (tp30) REVERT: V 12 LEU cc_start: 0.9590 (mt) cc_final: 0.8631 (mt) REVERT: W 24 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8462 (mm-30) REVERT: X 36 GLN cc_start: 0.8129 (pt0) cc_final: 0.7841 (pp30) REVERT: Y 3 GLU cc_start: 0.8890 (mp0) cc_final: 0.8426 (mm-30) REVERT: Z 29 LYS cc_start: 0.9370 (mmpt) cc_final: 0.9136 (mmmt) REVERT: a 3 GLU cc_start: 0.8835 (mp0) cc_final: 0.8560 (mm-30) REVERT: a 8 GLU cc_start: 0.8877 (pm20) cc_final: 0.8623 (pm20) REVERT: e 3 GLU cc_start: 0.8860 (mp0) cc_final: 0.8418 (mm-30) REVERT: j 19 LEU cc_start: 0.9248 (mt) cc_final: 0.8786 (tt) REVERT: j 29 LYS cc_start: 0.9314 (tptt) cc_final: 0.8718 (tmmt) REVERT: l 19 LEU cc_start: 0.9208 (mt) cc_final: 0.8532 (tt) REVERT: l 29 LYS cc_start: 0.9426 (mmmt) cc_final: 0.8906 (tmmt) REVERT: n 29 LYS cc_start: 0.9302 (mmtt) cc_final: 0.8888 (tmmt) outliers start: 2 outliers final: 0 residues processed: 471 average time/residue: 0.3901 time to fit residues: 226.4661 Evaluate side-chains 367 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 64 optimal weight: 0.0050 chunk 70 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 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 = 0.3451 r_free = 0.3451 target = 0.067046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057823 restraints weight = 52677.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059197 restraints weight = 37068.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060159 restraints weight = 28071.518| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.8565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11439 Z= 0.197 Angle : 0.912 9.079 15211 Z= 0.484 Chirality : 0.041 0.210 1927 Planarity : 0.004 0.073 1886 Dihedral : 6.387 69.615 1558 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1394 helix: 0.44 (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 C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 903) hydrogen bonds : angle 5.75306 ( 2709) covalent geometry : bond 0.00451 (11439) covalent geometry : angle 0.91236 (15211) ********************** 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 460 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 458 time to evaluate : 1.468 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: A 3 GLU cc_start: 0.8836 (mp0) cc_final: 0.8514 (mp0) REVERT: B 29 LYS cc_start: 0.9454 (mmmt) cc_final: 0.9130 (mmmt) REVERT: C 3 GLU cc_start: 0.8863 (mp0) cc_final: 0.8615 (mp0) REVERT: C 24 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8629 (mm-30) REVERT: F 29 LYS cc_start: 0.9266 (mmtm) cc_final: 0.9061 (mmmt) REVERT: G 29 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9176 (mmmt) REVERT: I 31 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8607 (mp0) REVERT: J 22 LYS cc_start: 0.9389 (ptpp) cc_final: 0.8948 (ptpp) REVERT: J 24 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8989 (mm-30) REVERT: J 31 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8988 (mm-30) REVERT: M 3 GLU cc_start: 0.8771 (mp0) cc_final: 0.8462 (mm-30) REVERT: M 24 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8806 (mm-30) REVERT: O 20 LYS cc_start: 0.9499 (ttmt) cc_final: 0.9247 (ttmt) REVERT: P 3 GLU cc_start: 0.8773 (mp0) cc_final: 0.8470 (mm-30) REVERT: S 3 GLU cc_start: 0.8616 (mp0) cc_final: 0.8368 (mm-30) REVERT: V 8 GLU cc_start: 0.9025 (tp30) cc_final: 0.8472 (tp30) REVERT: V 12 LEU cc_start: 0.9592 (mt) cc_final: 0.8625 (mt) REVERT: Y 3 GLU cc_start: 0.8876 (mp0) cc_final: 0.8418 (mm-30) REVERT: Z 29 LYS cc_start: 0.9406 (mmpt) cc_final: 0.9162 (mmmt) REVERT: a 3 GLU cc_start: 0.8848 (mp0) cc_final: 0.8581 (mm-30) REVERT: e 3 GLU cc_start: 0.8856 (mp0) cc_final: 0.8486 (mm-30) REVERT: j 19 LEU cc_start: 0.9288 (mt) cc_final: 0.8819 (tt) REVERT: j 29 LYS cc_start: 0.9270 (tptt) cc_final: 0.8701 (tmmt) REVERT: l 19 LEU cc_start: 0.9209 (mt) cc_final: 0.8518 (tt) REVERT: l 29 LYS cc_start: 0.9421 (mmmt) cc_final: 0.8916 (tmmt) REVERT: n 29 LYS cc_start: 0.9268 (mmtt) cc_final: 0.8893 (tmmt) REVERT: o 29 LYS cc_start: 0.8065 (mmpt) cc_final: 0.7768 (mmmt) outliers start: 2 outliers final: 1 residues processed: 458 average time/residue: 0.3942 time to fit residues: 222.4881 Evaluate side-chains 366 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 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 = 0.3418 r_free = 0.3418 target = 0.065282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.056076 restraints weight = 53444.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.057452 restraints weight = 37127.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058446 restraints weight = 27960.521| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.8549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11439 Z= 0.227 Angle : 0.942 9.299 15211 Z= 0.497 Chirality : 0.043 0.203 1927 Planarity : 0.004 0.035 1886 Dihedral : 6.484 70.572 1558 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.09 % Allowed : 1.54 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1394 helix: 0.18 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 6 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 903) hydrogen bonds : angle 5.98647 ( 2709) covalent geometry : bond 0.00505 (11439) covalent geometry : angle 0.94233 (15211) =============================================================================== Job complete usr+sys time: 5347.30 seconds wall clock time: 93 minutes 47.77 seconds (5627.77 seconds total)