Starting phenix.real_space_refine on Sat Dec 9 14:59:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/12_2023/6wl0_21814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/12_2023/6wl0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/12_2023/6wl0_21814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/12_2023/6wl0_21814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/12_2023/6wl0_21814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/12_2023/6wl0_21814.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11480 Number of models: 1 Model: "" Number of chains: 41 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} Chain: "B" 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} Chain: "C" 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} Chain: "D" 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} Chain: "E" 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} Chain: "F" 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} Chain: "G" 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} Chain: "H" 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} Chain: "I" 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} Chain: "J" 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} Chain: "K" 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} Chain: "L" 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} Chain: "M" 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} Chain: "N" 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} Chain: "O" 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} Chain: "P" 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} Chain: "Q" 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} Chain: "R" 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} Chain: "S" 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} Chain: "T" 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} Chain: "U" 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} Chain: "V" 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} Chain: "W" 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} Chain: "X" 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} Chain: "Y" 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} Chain: "Z" 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} 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} Chain: "b" 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} Chain: "c" 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} Chain: "d" 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} Chain: "e" 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} Chain: "f" 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} Chain: "g" 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} Chain: "h" 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} Chain: "i" 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} Chain: "j" 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} Chain: "k" 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} Chain: "l" 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} Chain: "m" 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} Chain: "n" 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} Chain: "o" 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} Time building chain proxies: 6.21, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.1 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: 0.76 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: 2.90 Time building geometry restraints manager: 4.90 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: 108.21 - 111.45: 5422 111.45 - 114.69: 2327 114.69 - 117.93: 1698 117.93 - 121.16: 3714 121.16 - 124.40: 2050 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 2.520 nonbonded pdb=" NH2 ARG R 10 " pdb=" OE1 GLU R 13 " model vdw 2.354 2.520 nonbonded pdb=" NH2 ARG J 10 " pdb=" OE1 GLU J 13 " model vdw 2.354 2.520 nonbonded pdb=" NH2 ARG l 10 " pdb=" OE1 GLU l 13 " model vdw 2.354 2.520 nonbonded pdb=" NH2 ARG F 10 " pdb=" OE1 GLU F 13 " model vdw 2.354 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.460 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.420 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- 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= 0.366 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 1.499 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 outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.4067 time to fit residues: 338.8523 Evaluate side-chains 359 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9327 ------------------------------------------------------------------------------- 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: 10.0000 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** X 36 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11439 Z= 0.232 Angle : 0.667 6.901 15211 Z= 0.363 Chirality : 0.034 0.115 1927 Planarity : 0.004 0.035 1886 Dihedral : 6.535 33.614 1558 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 15.59 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: -2.25 (0.21), residues: 1394 helix: -1.24 (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 f 10 *********************** 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 571 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 566 time to evaluate : 1.453 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 outliers start: 5 outliers final: 0 residues processed: 566 average time/residue: 0.4070 time to fit residues: 282.6355 Evaluate side-chains 406 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11439 Z= 0.214 Angle : 0.617 6.731 15211 Z= 0.334 Chirality : 0.034 0.113 1927 Planarity : 0.004 0.055 1886 Dihedral : 5.216 23.542 1558 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.45 % Allowed : 5.96 % Favored : 93.59 % 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: -0.73 (0.20), 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 0.011 0.001 ARG j 6 *********************** 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 566 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 561 time to evaluate : 1.547 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 outliers start: 5 outliers final: 1 residues processed: 562 average time/residue: 0.4289 time to fit residues: 294.5310 Evaluate side-chains 407 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 406 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1372 time to fit residues: 2.1224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 0.0980 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** ** F 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** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11439 Z= 0.196 Angle : 0.613 8.355 15211 Z= 0.331 Chirality : 0.033 0.182 1927 Planarity : 0.003 0.038 1886 Dihedral : 4.883 35.909 1558 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % 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: 0.46 (0.20), residues: 1394 helix: 0.43 (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 Q 10 *********************** 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 525 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 524 time to evaluate : 1.401 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 outliers start: 1 outliers final: 1 residues processed: 524 average time/residue: 0.4325 time to fit residues: 276.8777 Evaluate side-chains 385 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1398 time to fit residues: 2.1652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** D 36 GLN ** F 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** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11439 Z= 0.237 Angle : 0.679 6.485 15211 Z= 0.369 Chirality : 0.036 0.136 1927 Planarity : 0.004 0.038 1886 Dihedral : 4.906 37.987 1558 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.45 % Allowed : 5.06 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1394 helix: 0.70 (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 R 10 *********************** 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 492 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 487 time to evaluate : 1.492 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 outliers start: 5 outliers final: 0 residues processed: 488 average time/residue: 0.4370 time to fit residues: 261.3327 Evaluate side-chains 359 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 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 ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11439 Z= 0.247 Angle : 0.706 6.427 15211 Z= 0.384 Chirality : 0.037 0.161 1927 Planarity : 0.004 0.048 1886 Dihedral : 4.967 34.405 1558 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 3.88 % Favored : 95.84 % 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: 0.96 (0.20), residues: 1394 helix: 0.74 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 10 *********************** 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 462 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 459 time to evaluate : 1.438 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 outliers start: 3 outliers final: 2 residues processed: 459 average time/residue: 0.4472 time to fit residues: 250.0912 Evaluate side-chains 343 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 341 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1432 time to fit residues: 2.4422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.0670 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- 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** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11439 Z= 0.227 Angle : 0.713 8.281 15211 Z= 0.388 Chirality : 0.037 0.164 1927 Planarity : 0.004 0.059 1886 Dihedral : 4.831 28.672 1558 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.18 % Allowed : 2.53 % 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: 1.14 (0.20), residues: 1394 helix: 0.85 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 475 time to evaluate : 1.396 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 outliers start: 2 outliers final: 2 residues processed: 475 average time/residue: 0.4515 time to fit residues: 261.7741 Evaluate side-chains 349 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 347 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1657 time to fit residues: 2.6145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 113 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: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** X 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.8212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11439 Z= 0.293 Angle : 0.828 9.530 15211 Z= 0.446 Chirality : 0.039 0.173 1927 Planarity : 0.004 0.046 1886 Dihedral : 5.026 28.487 1558 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.18 % Allowed : 1.90 % Favored : 97.92 % 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: 0.46 (0.20), residues: 1394 helix: 0.43 (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 S 10 *********************** 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 454 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 452 time to evaluate : 1.473 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 outliers start: 2 outliers final: 2 residues processed: 452 average time/residue: 0.4315 time to fit residues: 237.6471 Evaluate side-chains 330 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 328 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1350 time to fit residues: 2.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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** D 36 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11439 Z= 0.258 Angle : 0.853 8.407 15211 Z= 0.454 Chirality : 0.040 0.184 1927 Planarity : 0.004 0.044 1886 Dihedral : 5.017 28.418 1558 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.27 % Allowed : 1.72 % Favored : 98.01 % 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: 0.53 (0.20), residues: 1394 helix: 0.47 (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 N 6 *********************** 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 472 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 469 time to evaluate : 1.359 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 outliers start: 3 outliers final: 1 residues processed: 469 average time/residue: 0.4262 time to fit residues: 243.2945 Evaluate side-chains 355 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1506 time to fit residues: 2.0272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- 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** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.8631 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= 0.288 Angle : 0.918 7.709 15211 Z= 0.491 Chirality : 0.042 0.192 1927 Planarity : 0.004 0.048 1886 Dihedral : 5.040 29.598 1558 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.18 % Allowed : 0.72 % Favored : 99.10 % 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: 0.22 (0.20), residues: 1394 helix: 0.28 (0.13), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Z 10 ********************** 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 455 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 453 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 453 average time/residue: 0.4311 time to fit residues: 237.6552 Evaluate side-chains 349 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 347 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1317 time to fit residues: 2.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 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 = 0.3746 r_free = 0.3746 target = 0.092267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.083456 restraints weight = 63591.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.084669 restraints weight = 36676.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.085472 restraints weight = 24237.718| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.8711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11439 Z= 0.289 Angle : 0.895 7.554 15211 Z= 0.475 Chirality : 0.043 0.379 1927 Planarity : 0.004 0.051 1886 Dihedral : 5.050 30.580 1558 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.18 % Allowed : 1.63 % Favored : 98.19 % 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: 0.15 (0.20), residues: 1394 helix: 0.24 (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 Z 10 =============================================================================== Job complete usr+sys time: 3968.61 seconds wall clock time: 71 minutes 42.72 seconds (4302.72 seconds total)