Starting phenix.real_space_refine on Fri Mar 15 10:54:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/03_2024/6wl0_21814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/03_2024/6wl0_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_21814/03_2024/6wl0_21814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/03_2024/6wl0_21814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/03_2024/6wl0_21814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl0_21814/03_2024/6wl0_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.47, per 1000 atoms: 0.56 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: 5.03 Conformation dependent library (CDL) restraints added in 2.0 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: 0.70 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: 2.75 Time building geometry restraints manager: 5.34 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: 0.570 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: 3.420 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 32.760 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.140 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- 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 : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8783 (mp0) cc_final: 0.8163 (mm-30) REVERT: A 10 ARG cc_start: 0.8751 (tpm170) cc_final: 0.8266 (tpm170) REVERT: A 32 ILE cc_start: 0.9162 (mt) cc_final: 0.8800 (mm) REVERT: B 27 LYS cc_start: 0.9399 (tmtt) cc_final: 0.9193 (tptp) REVERT: B 31 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9080 (mm-30) REVERT: C 19 LEU cc_start: 0.9524 (mt) cc_final: 0.9309 (mp) REVERT: C 31 GLU cc_start: 0.9388 (mm-30) cc_final: 0.8991 (mm-30) REVERT: D 2 LEU cc_start: 0.9049 (mp) cc_final: 0.8812 (mt) REVERT: D 3 GLU cc_start: 0.9068 (mp0) cc_final: 0.8786 (mp0) REVERT: D 10 ARG cc_start: 0.8964 (tpm170) cc_final: 0.7933 (tpm170) REVERT: D 13 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8441 (tm-30) REVERT: D 31 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8981 (mm-30) REVERT: E 31 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8990 (mm-30) REVERT: E 32 ILE cc_start: 0.9258 (mt) cc_final: 0.8907 (mm) REVERT: F 3 GLU cc_start: 0.8613 (mp0) cc_final: 0.8114 (mm-30) REVERT: F 10 ARG cc_start: 0.8686 (tpm170) cc_final: 0.8033 (tpm170) REVERT: F 13 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8428 (tm-30) REVERT: F 36 GLN cc_start: 0.8231 (mt0) cc_final: 0.7914 (pt0) REVERT: G 10 ARG cc_start: 0.8694 (tpm170) cc_final: 0.8247 (tpm170) REVERT: H 27 LYS cc_start: 0.9437 (tmtt) cc_final: 0.9083 (tptp) REVERT: H 31 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8960 (mm-30) REVERT: I 13 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8445 (tm-30) REVERT: I 31 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8909 (mm-30) REVERT: K 10 ARG cc_start: 0.8808 (tpm170) cc_final: 0.7828 (tpm170) REVERT: K 13 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8391 (tm-30) REVERT: L 10 ARG cc_start: 0.8699 (tpm170) cc_final: 0.8310 (tpm170) REVERT: M 3 GLU cc_start: 0.8883 (mp0) cc_final: 0.8330 (mm-30) REVERT: M 10 ARG cc_start: 0.8748 (tpm170) cc_final: 0.8374 (tpm170) REVERT: P 3 GLU cc_start: 0.8578 (mp0) cc_final: 0.7742 (mp0) REVERT: P 10 ARG cc_start: 0.8723 (tpm170) cc_final: 0.8388 (tpm170) REVERT: Q 10 ARG cc_start: 0.8630 (tpm170) cc_final: 0.8261 (tpm170) REVERT: R 10 ARG cc_start: 0.8493 (tpm170) cc_final: 0.7770 (tpm170) REVERT: R 36 GLN cc_start: 0.7781 (mt0) cc_final: 0.7335 (pt0) REVERT: S 3 GLU cc_start: 0.8650 (mp0) cc_final: 0.8287 (mm-30) REVERT: S 10 ARG cc_start: 0.8758 (tpm170) cc_final: 0.7913 (tpm170) REVERT: S 12 LEU cc_start: 0.9656 (mt) cc_final: 0.9456 (mm) REVERT: S 29 LYS cc_start: 0.9390 (tptt) cc_final: 0.9156 (tppt) REVERT: T 10 ARG cc_start: 0.8624 (tpm170) cc_final: 0.8246 (tpm170) REVERT: U 10 ARG cc_start: 0.8863 (tpm170) cc_final: 0.8418 (tpm170) REVERT: U 31 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8766 (mm-30) REVERT: V 3 GLU cc_start: 0.8776 (mp0) cc_final: 0.8008 (mp0) REVERT: V 10 ARG cc_start: 0.8673 (tpm170) cc_final: 0.8276 (tpm170) REVERT: V 12 LEU cc_start: 0.9595 (mt) cc_final: 0.9369 (mm) REVERT: V 36 GLN cc_start: 0.8194 (mt0) cc_final: 0.7974 (mt0) REVERT: W 3 GLU cc_start: 0.8721 (mp0) cc_final: 0.8387 (mm-30) REVERT: W 10 ARG cc_start: 0.8805 (tpm170) cc_final: 0.8523 (tpm170) REVERT: W 29 LYS cc_start: 0.9258 (tptt) cc_final: 0.9028 (tppt) REVERT: X 10 ARG cc_start: 0.8459 (tpm170) cc_final: 0.8117 (tpm170) REVERT: X 17 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9102 (mm-30) REVERT: X 32 ILE cc_start: 0.9451 (mt) cc_final: 0.9192 (tp) REVERT: Y 3 GLU cc_start: 0.8574 (mp0) cc_final: 0.8117 (mm-30) REVERT: Y 10 ARG cc_start: 0.8739 (tpm170) cc_final: 0.8427 (tpm170) REVERT: Z 10 ARG cc_start: 0.8652 (tpm170) cc_final: 0.8244 (tpm170) REVERT: Z 36 GLN cc_start: 0.8594 (mt0) cc_final: 0.8291 (pt0) REVERT: a 3 GLU cc_start: 0.8566 (mp0) cc_final: 0.8075 (mm-30) REVERT: a 33 LEU cc_start: 0.8055 (mt) cc_final: 0.7442 (mt) REVERT: b 10 ARG cc_start: 0.8764 (tpm170) cc_final: 0.7836 (tpm170) REVERT: b 13 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8209 (tm-30) REVERT: c 3 GLU cc_start: 0.8652 (mp0) cc_final: 0.8290 (mm-30) REVERT: d 10 ARG cc_start: 0.8531 (tpm170) cc_final: 0.8098 (tpm170) REVERT: d 17 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9090 (mm-30) REVERT: d 32 ILE cc_start: 0.9417 (mt) cc_final: 0.9196 (tp) REVERT: d 36 GLN cc_start: 0.8182 (mt0) cc_final: 0.7874 (pt0) REVERT: e 3 GLU cc_start: 0.8903 (mp0) cc_final: 0.8155 (mm-30) REVERT: f 27 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9227 (tptp) REVERT: f 31 GLU cc_start: 0.9465 (mm-30) cc_final: 0.8957 (mm-30) REVERT: g 3 GLU cc_start: 0.8862 (mp0) cc_final: 0.8556 (mp0) REVERT: h 10 ARG cc_start: 0.8667 (tpm170) cc_final: 0.8343 (tpm170) REVERT: i 3 GLU cc_start: 0.8575 (mp0) cc_final: 0.8333 (mm-30) REVERT: i 29 LYS cc_start: 0.9244 (tptt) cc_final: 0.8856 (tppt) REVERT: j 10 ARG cc_start: 0.8650 (tpm170) cc_final: 0.8242 (tpm170) REVERT: j 29 LYS cc_start: 0.9437 (tptt) cc_final: 0.9089 (tmmt) REVERT: k 3 GLU cc_start: 0.8648 (mp0) cc_final: 0.8257 (mm-30) REVERT: l 19 LEU cc_start: 0.9265 (mt) cc_final: 0.8761 (tt) REVERT: l 29 LYS cc_start: 0.9415 (tptt) cc_final: 0.9111 (tmmt) REVERT: l 31 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9044 (mm-30) REVERT: n 10 ARG cc_start: 0.8712 (tpm170) cc_final: 0.8230 (tpm170) REVERT: o 3 GLU cc_start: 0.8502 (mp0) cc_final: 0.8133 (mm-30) REVERT: o 32 ILE cc_start: 0.9096 (mt) cc_final: 0.8763 (tp) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.4054 time to fit residues: 335.7805 Evaluate side-chains 394 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4805 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= 0.244 Angle : 0.662 6.867 15211 Z= 0.360 Chirality : 0.034 0.122 1927 Planarity : 0.004 0.035 1886 Dihedral : 6.754 35.135 1558 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.45 % Allowed : 11.02 % Favored : 88.53 % 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: -2.27 (0.21), residues: 1394 helix: -1.25 (0.13), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 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 : 1.512 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: E 29 LYS cc_start: 0.9482 (mmpt) cc_final: 0.9112 (mmmt) REVERT: E 31 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8434 (mm-30) REVERT: F 3 GLU cc_start: 0.8638 (mp0) cc_final: 0.8415 (tp30) REVERT: G 3 GLU cc_start: 0.8995 (mp0) cc_final: 0.8589 (mp0) REVERT: I 8 GLU cc_start: 0.9265 (mp0) cc_final: 0.9062 (mp0) REVERT: I 29 LYS cc_start: 0.9497 (mmpt) cc_final: 0.9152 (mmmt) REVERT: J 29 LYS cc_start: 0.9443 (mmtt) cc_final: 0.9172 (mmmt) REVERT: M 3 GLU cc_start: 0.8890 (mp0) cc_final: 0.8490 (tp30) REVERT: O 10 ARG cc_start: 0.8812 (tpm170) cc_final: 0.8386 (mmm160) REVERT: O 29 LYS cc_start: 0.9443 (mmpt) cc_final: 0.9149 (tppt) REVERT: P 3 GLU cc_start: 0.8697 (mp0) cc_final: 0.8076 (mp0) REVERT: R 12 LEU cc_start: 0.9598 (tt) cc_final: 0.9186 (tp) REVERT: R 24 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8917 (mm-30) REVERT: U 29 LYS cc_start: 0.9330 (mmpt) cc_final: 0.8979 (tppt) REVERT: V 12 LEU cc_start: 0.9705 (mt) cc_final: 0.8875 (mt) REVERT: W 3 GLU cc_start: 0.8839 (mp0) cc_final: 0.8616 (mm-30) REVERT: Y 3 GLU cc_start: 0.8635 (mp0) cc_final: 0.8321 (mm-30) REVERT: b 27 LYS cc_start: 0.9463 (tmmt) cc_final: 0.9261 (ttpp) REVERT: c 3 GLU cc_start: 0.8689 (mp0) cc_final: 0.8346 (tp30) REVERT: d 36 GLN cc_start: 0.8340 (mt0) cc_final: 0.7946 (tt0) REVERT: e 27 LYS cc_start: 0.9532 (tmmt) cc_final: 0.9301 (ttpp) REVERT: f 10 ARG cc_start: 0.8618 (mmp80) cc_final: 0.8390 (mmp80) REVERT: f 29 LYS cc_start: 0.9544 (tppt) cc_final: 0.9253 (mmmt) REVERT: g 3 GLU cc_start: 0.9049 (mp0) cc_final: 0.8841 (mp0) REVERT: i 3 GLU cc_start: 0.8849 (mp0) cc_final: 0.8634 (tp30) REVERT: j 8 GLU cc_start: 0.8801 (pp20) cc_final: 0.8563 (pp20) REVERT: j 29 LYS cc_start: 0.9551 (tptt) cc_final: 0.9083 (tmmt) REVERT: k 3 GLU cc_start: 0.8896 (mp0) cc_final: 0.8666 (tp30) REVERT: k 24 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8950 (mm-30) REVERT: l 3 GLU cc_start: 0.8942 (mp0) cc_final: 0.8600 (mp0) REVERT: l 19 LEU cc_start: 0.9225 (mt) cc_final: 0.8610 (tp) REVERT: l 29 LYS cc_start: 0.9459 (tptt) cc_final: 0.9033 (tmmt) REVERT: n 29 LYS cc_start: 0.9417 (mmtt) cc_final: 0.8996 (tmmt) REVERT: o 3 GLU cc_start: 0.8780 (mp0) cc_final: 0.8405 (tp30) REVERT: o 24 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9185 (mm-30) outliers start: 5 outliers final: 0 residues processed: 566 average time/residue: 0.4040 time to fit residues: 280.5234 Evaluate side-chains 414 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8708 moved from start: 0.6141 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= 0.247 Angle : 0.654 7.982 15211 Z= 0.353 Chirality : 0.035 0.123 1927 Planarity : 0.004 0.051 1886 Dihedral : 5.485 37.649 1558 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.45 % Allowed : 5.15 % Favored : 94.40 % 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: -0.90 (0.19), residues: 1394 helix: -0.41 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 10 *********************** 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 560 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 555 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8788 (mp0) cc_final: 0.8438 (mm-30) REVERT: B 36 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.5833 (pp30) REVERT: C 3 GLU cc_start: 0.9012 (mp0) cc_final: 0.8688 (mm-30) REVERT: C 10 ARG cc_start: 0.8687 (mmp80) cc_final: 0.8314 (mmp80) REVERT: D 3 GLU cc_start: 0.9040 (mp0) cc_final: 0.8666 (mm-30) REVERT: D 10 ARG cc_start: 0.8875 (mmp-170) cc_final: 0.8670 (mmp80) REVERT: F 3 GLU cc_start: 0.8783 (mp0) cc_final: 0.8536 (mm-30) REVERT: G 3 GLU cc_start: 0.9070 (mp0) cc_final: 0.8694 (mm-30) REVERT: H 3 GLU cc_start: 0.9101 (mp0) cc_final: 0.8830 (mm-30) REVERT: I 3 GLU cc_start: 0.9127 (mp0) cc_final: 0.8888 (mm-30) REVERT: I 8 GLU cc_start: 0.9266 (mp0) cc_final: 0.9044 (mp0) REVERT: J 3 GLU cc_start: 0.8938 (mp0) cc_final: 0.8703 (mm-30) REVERT: K 13 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8537 (tm-30) REVERT: K 29 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9221 (mmmt) REVERT: L 3 GLU cc_start: 0.9028 (mp0) cc_final: 0.8653 (mm-30) REVERT: M 3 GLU cc_start: 0.8788 (mp0) cc_final: 0.8430 (mm-30) REVERT: M 13 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8503 (tm-30) REVERT: N 3 GLU cc_start: 0.9023 (mp0) cc_final: 0.8777 (mm-30) REVERT: N 8 GLU cc_start: 0.9190 (mp0) cc_final: 0.8955 (mp0) REVERT: N 13 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8508 (tm-30) REVERT: N 29 LYS cc_start: 0.9358 (mmmt) cc_final: 0.9089 (mmmt) REVERT: P 3 GLU cc_start: 0.8839 (mp0) cc_final: 0.8325 (mm-30) REVERT: P 36 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.5778 (pp30) REVERT: Q 3 GLU cc_start: 0.9104 (mp0) cc_final: 0.8704 (mm-30) REVERT: Q 13 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8807 (tm-30) REVERT: Q 36 GLN cc_start: 0.7527 (mp10) cc_final: 0.7186 (mp10) REVERT: R 3 GLU cc_start: 0.9074 (mp0) cc_final: 0.8683 (mm-30) REVERT: S 3 GLU cc_start: 0.8944 (mp0) cc_final: 0.8576 (mm-30) REVERT: T 3 GLU cc_start: 0.8838 (mp0) cc_final: 0.8460 (mm-30) REVERT: U 3 GLU cc_start: 0.9128 (mp0) cc_final: 0.8892 (mm-30) REVERT: U 13 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8526 (tm-30) REVERT: U 29 LYS cc_start: 0.9364 (mmpt) cc_final: 0.9147 (tppt) REVERT: V 13 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8385 (tm-30) REVERT: W 3 GLU cc_start: 0.8899 (mp0) cc_final: 0.8694 (mm-30) REVERT: X 36 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.5167 (pp30) REVERT: Y 3 GLU cc_start: 0.8721 (mp0) cc_final: 0.8183 (tp30) REVERT: a 3 GLU cc_start: 0.9022 (mp0) cc_final: 0.8620 (mm-30) REVERT: c 3 GLU cc_start: 0.8636 (mp0) cc_final: 0.8403 (mm-30) REVERT: d 36 GLN cc_start: 0.8409 (mt0) cc_final: 0.8156 (tt0) REVERT: f 3 GLU cc_start: 0.9012 (mp0) cc_final: 0.8517 (mm-30) REVERT: f 29 LYS cc_start: 0.9584 (tppt) cc_final: 0.9288 (mmmt) REVERT: g 3 GLU cc_start: 0.9109 (mp0) cc_final: 0.8863 (mm-30) REVERT: i 3 GLU cc_start: 0.8983 (mp0) cc_final: 0.8773 (mm-30) REVERT: j 29 LYS cc_start: 0.9555 (tptt) cc_final: 0.9040 (tmmt) REVERT: k 3 GLU cc_start: 0.8951 (mp0) cc_final: 0.8739 (mm-30) REVERT: l 13 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8833 (tm-30) REVERT: l 19 LEU cc_start: 0.9214 (mt) cc_final: 0.8630 (tp) REVERT: l 29 LYS cc_start: 0.9472 (tptt) cc_final: 0.9023 (tmmt) REVERT: m 3 GLU cc_start: 0.8790 (pp20) cc_final: 0.8216 (mm-30) REVERT: m 13 GLU cc_start: 0.9404 (pp20) cc_final: 0.8964 (pp20) REVERT: m 29 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8339 (mmmt) REVERT: n 13 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8833 (tm-30) REVERT: n 29 LYS cc_start: 0.9400 (mmtt) cc_final: 0.8969 (tmmt) REVERT: o 3 GLU cc_start: 0.9047 (mp0) cc_final: 0.8640 (mm-30) outliers start: 5 outliers final: 1 residues processed: 556 average time/residue: 0.4200 time to fit residues: 285.4651 Evaluate side-chains 423 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 419 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 GLN ** a 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11439 Z= 0.214 Angle : 0.620 8.096 15211 Z= 0.336 Chirality : 0.034 0.123 1927 Planarity : 0.004 0.044 1886 Dihedral : 5.158 23.145 1558 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % 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: 0.21 (0.20), residues: 1394 helix: 0.28 (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 I 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 544 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 540 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8846 (mp0) cc_final: 0.8471 (mm-30) REVERT: B 29 LYS cc_start: 0.9497 (mmpt) cc_final: 0.9073 (mmmt) REVERT: C 3 GLU cc_start: 0.9031 (mp0) cc_final: 0.8606 (mm-30) REVERT: C 10 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8338 (mmp80) REVERT: D 3 GLU cc_start: 0.9041 (mp0) cc_final: 0.8634 (mm-30) REVERT: F 3 GLU cc_start: 0.8870 (mp0) cc_final: 0.8579 (mm-30) REVERT: G 3 GLU cc_start: 0.9039 (mp0) cc_final: 0.8747 (mm-30) REVERT: G 29 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9233 (mmmt) REVERT: H 3 GLU cc_start: 0.9107 (mp0) cc_final: 0.8768 (mm-30) REVERT: I 10 ARG cc_start: 0.9219 (mmm-85) cc_final: 0.8841 (mmm-85) REVERT: J 3 GLU cc_start: 0.8998 (mp0) cc_final: 0.8667 (mm-30) REVERT: K 13 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8628 (tm-30) REVERT: L 36 GLN cc_start: 0.6733 (pp30) cc_final: 0.6089 (pp30) REVERT: M 3 GLU cc_start: 0.8895 (mp0) cc_final: 0.8520 (mm-30) REVERT: N 3 GLU cc_start: 0.9000 (mp0) cc_final: 0.8786 (mm-30) REVERT: N 13 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8728 (tm-30) REVERT: N 29 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9159 (mmmt) REVERT: P 31 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8908 (tp30) REVERT: Q 3 GLU cc_start: 0.9117 (mp0) cc_final: 0.8711 (mm-30) REVERT: R 3 GLU cc_start: 0.9063 (mp0) cc_final: 0.8659 (mm-30) REVERT: R 12 LEU cc_start: 0.9625 (tt) cc_final: 0.9390 (tp) REVERT: S 3 GLU cc_start: 0.8932 (mp0) cc_final: 0.8511 (mm-30) REVERT: T 24 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8758 (mm-30) REVERT: T 29 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9139 (mmmt) REVERT: U 3 GLU cc_start: 0.9165 (mp0) cc_final: 0.8885 (mm-30) REVERT: Y 3 GLU cc_start: 0.8869 (mp0) cc_final: 0.8474 (mm-30) REVERT: Y 31 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8960 (mm-30) REVERT: a 3 GLU cc_start: 0.9091 (mp0) cc_final: 0.8633 (mm-30) REVERT: c 29 LYS cc_start: 0.9394 (mmpt) cc_final: 0.9062 (mppt) REVERT: d 36 GLN cc_start: 0.8181 (mt0) cc_final: 0.7907 (tt0) REVERT: f 3 GLU cc_start: 0.9033 (mp0) cc_final: 0.8595 (mm-30) REVERT: g 3 GLU cc_start: 0.9117 (mp0) cc_final: 0.8834 (mm-30) REVERT: h 29 LYS cc_start: 0.9432 (mmpt) cc_final: 0.9211 (mmmt) REVERT: i 3 GLU cc_start: 0.9033 (mp0) cc_final: 0.8805 (mm-30) REVERT: j 3 GLU cc_start: 0.8996 (mp0) cc_final: 0.8704 (mm-30) REVERT: j 29 LYS cc_start: 0.9497 (tptt) cc_final: 0.8981 (tmmt) REVERT: k 3 GLU cc_start: 0.8878 (mp0) cc_final: 0.8656 (mm-30) REVERT: l 19 LEU cc_start: 0.9219 (mt) cc_final: 0.8609 (tp) REVERT: l 29 LYS cc_start: 0.9489 (tptt) cc_final: 0.9046 (tmmt) REVERT: m 3 GLU cc_start: 0.8812 (pp20) cc_final: 0.8286 (mm-30) REVERT: n 29 LYS cc_start: 0.9315 (mmtt) cc_final: 0.8880 (tmmt) REVERT: o 3 GLU cc_start: 0.9060 (mp0) cc_final: 0.8607 (mm-30) outliers start: 4 outliers final: 1 residues processed: 540 average time/residue: 0.4062 time to fit residues: 269.3007 Evaluate side-chains 415 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** 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 Z 36 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11439 Z= 0.215 Angle : 0.642 7.186 15211 Z= 0.350 Chirality : 0.035 0.142 1927 Planarity : 0.004 0.051 1886 Dihedral : 5.027 22.134 1558 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.27 % Allowed : 4.16 % Favored : 95.57 % 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: 1.02 (0.20), residues: 1394 helix: 0.78 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG j 6 *********************** 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 521 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 518 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8895 (mp0) cc_final: 0.8485 (tp30) REVERT: C 3 GLU cc_start: 0.8990 (mp0) cc_final: 0.8575 (mm-30) REVERT: D 3 GLU cc_start: 0.9018 (mp0) cc_final: 0.8636 (mm-30) REVERT: F 3 GLU cc_start: 0.8918 (mp0) cc_final: 0.8596 (mm-30) REVERT: F 29 LYS cc_start: 0.9290 (mmtm) cc_final: 0.9081 (mmmt) REVERT: G 3 GLU cc_start: 0.9069 (mp0) cc_final: 0.8774 (mm-30) REVERT: G 29 LYS cc_start: 0.9492 (mmmt) cc_final: 0.9006 (mmmt) REVERT: H 3 GLU cc_start: 0.9085 (mp0) cc_final: 0.8750 (mm-30) REVERT: H 8 GLU cc_start: 0.9259 (mp0) cc_final: 0.9030 (mp0) REVERT: I 29 LYS cc_start: 0.9481 (mmmt) cc_final: 0.8928 (mmmt) REVERT: I 32 ILE cc_start: 0.9214 (mm) cc_final: 0.8969 (mt) REVERT: J 3 GLU cc_start: 0.9041 (mp0) cc_final: 0.8783 (mm-30) REVERT: L 3 GLU cc_start: 0.9083 (mp0) cc_final: 0.8708 (mm-30) REVERT: M 3 GLU cc_start: 0.8917 (mp0) cc_final: 0.8532 (mm-30) REVERT: N 3 GLU cc_start: 0.8987 (mp0) cc_final: 0.8768 (mm-30) REVERT: N 29 LYS cc_start: 0.9372 (mmmt) cc_final: 0.9161 (mmmt) REVERT: P 3 GLU cc_start: 0.8863 (mp0) cc_final: 0.8116 (mp0) REVERT: Q 3 GLU cc_start: 0.9131 (mp0) cc_final: 0.8712 (mm-30) REVERT: Q 29 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9133 (mmmt) REVERT: R 12 LEU cc_start: 0.9613 (tt) cc_final: 0.9389 (tp) REVERT: R 24 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8744 (mm-30) REVERT: S 3 GLU cc_start: 0.8960 (mp0) cc_final: 0.8564 (mm-30) REVERT: T 24 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8775 (mm-30) REVERT: U 3 GLU cc_start: 0.9139 (mp0) cc_final: 0.8902 (mp0) REVERT: U 29 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9070 (tppt) REVERT: X 33 LEU cc_start: 0.7832 (mt) cc_final: 0.7483 (mt) REVERT: X 36 GLN cc_start: 0.8125 (pt0) cc_final: 0.7854 (pp30) REVERT: Y 3 GLU cc_start: 0.8991 (mp0) cc_final: 0.8582 (mm-30) REVERT: Y 29 LYS cc_start: 0.9397 (mmpt) cc_final: 0.9191 (mmmt) REVERT: Z 29 LYS cc_start: 0.9473 (mmpt) cc_final: 0.9175 (mmmt) REVERT: a 3 GLU cc_start: 0.9109 (mp0) cc_final: 0.8659 (mm-30) REVERT: b 3 GLU cc_start: 0.8992 (mp0) cc_final: 0.8383 (mp0) REVERT: d 3 GLU cc_start: 0.8955 (mp0) cc_final: 0.8588 (mm-30) REVERT: e 3 GLU cc_start: 0.9142 (mp0) cc_final: 0.8496 (mm-30) REVERT: f 3 GLU cc_start: 0.9061 (mp0) cc_final: 0.8657 (mm-30) REVERT: g 3 GLU cc_start: 0.9083 (mp0) cc_final: 0.8825 (mm-30) REVERT: g 33 LEU cc_start: 0.8261 (tt) cc_final: 0.7989 (tt) REVERT: i 3 GLU cc_start: 0.9061 (mp0) cc_final: 0.8813 (mm-30) REVERT: j 29 LYS cc_start: 0.9399 (tptt) cc_final: 0.8794 (tmmt) REVERT: k 3 GLU cc_start: 0.8950 (mp0) cc_final: 0.8695 (mm-30) REVERT: l 19 LEU cc_start: 0.9206 (mt) cc_final: 0.8577 (tp) REVERT: l 29 LYS cc_start: 0.9477 (tptt) cc_final: 0.9014 (tmmt) REVERT: m 3 GLU cc_start: 0.8772 (pp20) cc_final: 0.8263 (mm-30) REVERT: n 29 LYS cc_start: 0.9311 (mmtt) cc_final: 0.8845 (tmmt) REVERT: o 3 GLU cc_start: 0.9068 (mp0) cc_final: 0.8625 (mm-30) outliers start: 3 outliers final: 1 residues processed: 518 average time/residue: 0.4147 time to fit residues: 263.0688 Evaluate side-chains 383 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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: 10.0000 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 114 optimal weight: 0.0970 overall best weight: 4.8186 ------------------------------------------------------------------------------- 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** H 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN X 36 GLN ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.7634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11439 Z= 0.242 Angle : 0.693 6.922 15211 Z= 0.376 Chirality : 0.036 0.157 1927 Planarity : 0.004 0.074 1886 Dihedral : 4.958 24.721 1558 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.18 % Allowed : 4.16 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1394 helix: 0.87 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 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 488 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 486 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8952 (mp0) cc_final: 0.8631 (mp0) REVERT: B 29 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9087 (mmmt) REVERT: C 3 GLU cc_start: 0.8986 (mp0) cc_final: 0.8563 (mm-30) REVERT: D 3 GLU cc_start: 0.9028 (mp0) cc_final: 0.8622 (mm-30) REVERT: D 29 LYS cc_start: 0.9358 (mmpt) cc_final: 0.9150 (mmmt) REVERT: E 10 ARG cc_start: 0.8977 (ttt-90) cc_final: 0.8586 (ttt180) REVERT: F 3 GLU cc_start: 0.8925 (mp0) cc_final: 0.8621 (mm-30) REVERT: F 29 LYS cc_start: 0.9241 (mmtm) cc_final: 0.8980 (mmmt) REVERT: G 3 GLU cc_start: 0.9058 (mp0) cc_final: 0.8831 (mm-30) REVERT: G 29 LYS cc_start: 0.9514 (mmmt) cc_final: 0.9052 (mmmt) REVERT: H 29 LYS cc_start: 0.9487 (tppt) cc_final: 0.9222 (mmmt) REVERT: I 8 GLU cc_start: 0.9249 (mp0) cc_final: 0.9019 (mp0) REVERT: I 29 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9124 (mmmt) REVERT: J 3 GLU cc_start: 0.9040 (mp0) cc_final: 0.8749 (mm-30) REVERT: K 3 GLU cc_start: 0.9066 (mp0) cc_final: 0.8823 (mp0) REVERT: L 29 LYS cc_start: 0.9332 (mmmt) cc_final: 0.9116 (mmmt) REVERT: N 3 GLU cc_start: 0.9012 (mp0) cc_final: 0.8799 (mm-30) REVERT: O 29 LYS cc_start: 0.9463 (mmpt) cc_final: 0.9103 (mmmt) REVERT: R 3 GLU cc_start: 0.9020 (mp0) cc_final: 0.8759 (mm-30) REVERT: R 12 LEU cc_start: 0.9620 (tt) cc_final: 0.9368 (tp) REVERT: R 24 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8785 (mm-30) REVERT: S 3 GLU cc_start: 0.8983 (mp0) cc_final: 0.8663 (mm-30) REVERT: T 29 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9124 (mmmt) REVERT: U 3 GLU cc_start: 0.9140 (mp0) cc_final: 0.8894 (mp0) REVERT: U 17 GLU cc_start: 0.9051 (mp0) cc_final: 0.8831 (mp0) REVERT: W 31 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8884 (tp30) REVERT: Y 3 GLU cc_start: 0.8996 (mp0) cc_final: 0.8543 (tp30) REVERT: Z 29 LYS cc_start: 0.9503 (mmpt) cc_final: 0.9128 (mmmt) REVERT: a 3 GLU cc_start: 0.9113 (mp0) cc_final: 0.8678 (mm-30) REVERT: b 3 GLU cc_start: 0.9043 (mp0) cc_final: 0.8479 (mp0) REVERT: b 32 ILE cc_start: 0.9106 (mt) cc_final: 0.8876 (mt) REVERT: e 3 GLU cc_start: 0.9170 (mp0) cc_final: 0.8564 (mm-30) REVERT: f 3 GLU cc_start: 0.9016 (mp0) cc_final: 0.8741 (mp0) REVERT: g 3 GLU cc_start: 0.9148 (mp0) cc_final: 0.8907 (mm-30) REVERT: g 29 LYS cc_start: 0.9370 (mmpt) cc_final: 0.9115 (tppt) REVERT: h 29 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9201 (mmmt) REVERT: i 3 GLU cc_start: 0.9056 (mp0) cc_final: 0.8833 (mm-30) REVERT: j 29 LYS cc_start: 0.9452 (tptt) cc_final: 0.8828 (tmmt) REVERT: k 3 GLU cc_start: 0.8919 (mp0) cc_final: 0.8654 (mm-30) REVERT: l 19 LEU cc_start: 0.9185 (mt) cc_final: 0.8649 (tt) REVERT: l 29 LYS cc_start: 0.9451 (tptt) cc_final: 0.8949 (tmmt) REVERT: m 3 GLU cc_start: 0.8808 (pp20) cc_final: 0.8245 (mm-30) REVERT: n 3 GLU cc_start: 0.9039 (mp0) cc_final: 0.8747 (mm-30) REVERT: n 29 LYS cc_start: 0.9302 (mmtt) cc_final: 0.8847 (tmmt) REVERT: o 3 GLU cc_start: 0.9039 (mp0) cc_final: 0.8619 (mm-30) outliers start: 2 outliers final: 1 residues processed: 486 average time/residue: 0.4295 time to fit residues: 254.3498 Evaluate side-chains 363 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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: 2.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** T 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11439 Z= 0.263 Angle : 0.744 9.836 15211 Z= 0.403 Chirality : 0.038 0.190 1927 Planarity : 0.004 0.048 1886 Dihedral : 5.103 31.072 1558 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % 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: 0.93 (0.20), residues: 1394 helix: 0.72 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 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: 1 poor density : 476 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 revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8946 (mp0) cc_final: 0.8628 (mp0) REVERT: B 29 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9157 (mmmt) REVERT: C 3 GLU cc_start: 0.9005 (mp0) cc_final: 0.8573 (mm-30) REVERT: D 3 GLU cc_start: 0.9015 (mp0) cc_final: 0.8614 (mm-30) REVERT: D 29 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9166 (mmmt) REVERT: F 3 GLU cc_start: 0.8937 (mp0) cc_final: 0.8613 (mm-30) REVERT: G 29 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9201 (mmmt) REVERT: H 3 GLU cc_start: 0.9131 (mp0) cc_final: 0.8779 (mm-30) REVERT: L 3 GLU cc_start: 0.9095 (mp0) cc_final: 0.8817 (mm-30) REVERT: N 3 GLU cc_start: 0.9017 (mp0) cc_final: 0.8789 (mm-30) REVERT: O 29 LYS cc_start: 0.9445 (mmpt) cc_final: 0.9093 (mmmt) REVERT: P 3 GLU cc_start: 0.9026 (mp0) cc_final: 0.8778 (mp0) REVERT: Q 3 GLU cc_start: 0.9142 (mp0) cc_final: 0.8707 (mm-30) REVERT: Q 29 LYS cc_start: 0.9360 (mmmt) cc_final: 0.9144 (mmmt) REVERT: R 12 LEU cc_start: 0.9617 (tt) cc_final: 0.9363 (tp) REVERT: R 29 LYS cc_start: 0.9374 (mmmt) cc_final: 0.9147 (mmmt) REVERT: R 34 LYS cc_start: 0.9386 (tptp) cc_final: 0.8959 (tptp) REVERT: S 3 GLU cc_start: 0.8960 (mp0) cc_final: 0.8676 (mm-30) REVERT: T 29 LYS cc_start: 0.9485 (mmmt) cc_final: 0.9216 (mmmt) REVERT: U 3 GLU cc_start: 0.9124 (mp0) cc_final: 0.8848 (mp0) REVERT: U 17 GLU cc_start: 0.9137 (mp0) cc_final: 0.8800 (mp0) REVERT: V 24 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8558 (mm-30) REVERT: Z 29 LYS cc_start: 0.9488 (mmpt) cc_final: 0.9177 (mmmt) REVERT: a 3 GLU cc_start: 0.9138 (mp0) cc_final: 0.8667 (mm-30) REVERT: b 3 GLU cc_start: 0.9096 (mp0) cc_final: 0.8529 (mp0) REVERT: e 3 GLU cc_start: 0.9181 (mp0) cc_final: 0.8569 (mm-30) REVERT: f 3 GLU cc_start: 0.8917 (mp0) cc_final: 0.8559 (mp0) REVERT: g 3 GLU cc_start: 0.9129 (mp0) cc_final: 0.8905 (mm-30) REVERT: g 29 LYS cc_start: 0.9378 (mmpt) cc_final: 0.8943 (mmmt) REVERT: h 29 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9119 (mmmt) REVERT: i 3 GLU cc_start: 0.9059 (mp0) cc_final: 0.8850 (mm-30) REVERT: j 29 LYS cc_start: 0.9467 (tptt) cc_final: 0.8838 (tmmt) REVERT: k 3 GLU cc_start: 0.8924 (mp0) cc_final: 0.8675 (mm-30) REVERT: l 19 LEU cc_start: 0.9158 (mt) cc_final: 0.8596 (tt) REVERT: l 29 LYS cc_start: 0.9441 (tptt) cc_final: 0.8929 (tmmt) REVERT: m 3 GLU cc_start: 0.8816 (pp20) cc_final: 0.8245 (mm-30) REVERT: n 3 GLU cc_start: 0.9020 (mp0) cc_final: 0.8731 (mm-30) REVERT: n 29 LYS cc_start: 0.9325 (mmtt) cc_final: 0.8880 (tmmt) REVERT: o 3 GLU cc_start: 0.9023 (mp0) cc_final: 0.8601 (mm-30) outliers start: 1 outliers final: 1 residues processed: 476 average time/residue: 0.4077 time to fit residues: 237.0323 Evaluate side-chains 349 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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: 20.0000 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.7900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11439 Z= 0.307 Angle : 0.818 8.803 15211 Z= 0.443 Chirality : 0.040 0.175 1927 Planarity : 0.004 0.045 1886 Dihedral : 5.371 42.085 1558 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % 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: 0.42 (0.20), residues: 1394 helix: 0.41 (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 d 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 459 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 458 time to evaluate : 1.361 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: A 3 GLU cc_start: 0.8941 (mp0) cc_final: 0.8606 (mp0) REVERT: B 29 LYS cc_start: 0.9460 (mmmt) cc_final: 0.9139 (mmmt) REVERT: C 3 GLU cc_start: 0.8997 (mp0) cc_final: 0.8554 (mm-30) REVERT: D 3 GLU cc_start: 0.9078 (mp0) cc_final: 0.8685 (mm-30) REVERT: F 3 GLU cc_start: 0.8944 (mp0) cc_final: 0.8617 (mm-30) REVERT: F 29 LYS cc_start: 0.9562 (mmmm) cc_final: 0.9127 (mmmt) REVERT: G 29 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9205 (mmmt) REVERT: H 3 GLU cc_start: 0.9108 (mp0) cc_final: 0.8752 (mm-30) REVERT: I 8 GLU cc_start: 0.9241 (mp0) cc_final: 0.9038 (mp0) REVERT: K 3 GLU cc_start: 0.8944 (mp0) cc_final: 0.8724 (mp0) REVERT: L 3 GLU cc_start: 0.9120 (mp0) cc_final: 0.8844 (mm-30) REVERT: N 3 GLU cc_start: 0.8997 (mp0) cc_final: 0.8790 (mm-30) REVERT: N 22 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8651 (ptpp) REVERT: O 29 LYS cc_start: 0.9431 (mmpt) cc_final: 0.9156 (mmmt) REVERT: P 3 GLU cc_start: 0.9031 (mp0) cc_final: 0.8782 (mp0) REVERT: Q 3 GLU cc_start: 0.9158 (mp0) cc_final: 0.8693 (mm-30) REVERT: S 3 GLU cc_start: 0.8946 (mp0) cc_final: 0.8659 (mm-30) REVERT: T 29 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9273 (mmmt) REVERT: U 3 GLU cc_start: 0.9119 (mp0) cc_final: 0.8840 (mp0) REVERT: U 17 GLU cc_start: 0.9223 (mp0) cc_final: 0.8927 (mp0) REVERT: Z 29 LYS cc_start: 0.9471 (mmpt) cc_final: 0.9158 (mmmt) REVERT: a 3 GLU cc_start: 0.9136 (mp0) cc_final: 0.8677 (mm-30) REVERT: b 34 LYS cc_start: 0.8411 (tppt) cc_final: 0.8113 (tppt) REVERT: e 3 GLU cc_start: 0.9157 (mp0) cc_final: 0.8554 (mm-30) REVERT: f 3 GLU cc_start: 0.9011 (mp0) cc_final: 0.8654 (mp0) REVERT: g 3 GLU cc_start: 0.9137 (mp0) cc_final: 0.8914 (mm-30) REVERT: h 29 LYS cc_start: 0.9422 (mmmt) cc_final: 0.9172 (mmtp) REVERT: i 3 GLU cc_start: 0.9076 (mp0) cc_final: 0.8840 (mm-30) REVERT: j 29 LYS cc_start: 0.9490 (tptt) cc_final: 0.8855 (tmmt) REVERT: k 3 GLU cc_start: 0.8943 (mp0) cc_final: 0.8682 (mm-30) REVERT: l 19 LEU cc_start: 0.9110 (mt) cc_final: 0.8536 (tt) REVERT: l 29 LYS cc_start: 0.9437 (tptt) cc_final: 0.8988 (tmmt) REVERT: m 3 GLU cc_start: 0.8803 (pp20) cc_final: 0.8270 (mm-30) REVERT: n 3 GLU cc_start: 0.9007 (mp0) cc_final: 0.8677 (mm-30) REVERT: n 29 LYS cc_start: 0.9344 (mmtt) cc_final: 0.8943 (pttp) REVERT: o 3 GLU cc_start: 0.9021 (mp0) cc_final: 0.8636 (mm-30) outliers start: 1 outliers final: 1 residues processed: 458 average time/residue: 0.4153 time to fit residues: 232.9188 Evaluate side-chains 335 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 334 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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: 6.9990 chunk 110 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.8136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11439 Z= 0.298 Angle : 0.860 8.021 15211 Z= 0.464 Chirality : 0.041 0.247 1927 Planarity : 0.004 0.042 1886 Dihedral : 5.483 44.245 1558 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.29 (0.20), residues: 1394 helix: 0.33 (0.12), residues: 1394 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 10 *********************** 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 479 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8949 (mp0) cc_final: 0.8621 (mp0) REVERT: B 29 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9016 (mmmt) REVERT: C 3 GLU cc_start: 0.8989 (mp0) cc_final: 0.8531 (mm-30) REVERT: D 3 GLU cc_start: 0.9055 (mp0) cc_final: 0.8680 (mm-30) REVERT: F 3 GLU cc_start: 0.8989 (mp0) cc_final: 0.8693 (mm-30) REVERT: F 29 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9225 (mmtp) REVERT: G 29 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9203 (mmmt) REVERT: H 3 GLU cc_start: 0.9136 (mp0) cc_final: 0.8796 (mm-30) REVERT: K 10 ARG cc_start: 0.8537 (mmp80) cc_final: 0.8165 (mmp80) REVERT: K 29 LYS cc_start: 0.9485 (mmmt) cc_final: 0.9270 (mmmt) REVERT: L 3 GLU cc_start: 0.9101 (mp0) cc_final: 0.8837 (mm-30) REVERT: O 29 LYS cc_start: 0.9419 (mmpt) cc_final: 0.9179 (mmmt) REVERT: P 3 GLU cc_start: 0.9037 (mp0) cc_final: 0.8827 (mp0) REVERT: P 24 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8911 (mm-30) REVERT: Q 3 GLU cc_start: 0.9120 (mp0) cc_final: 0.8743 (mm-30) REVERT: Q 29 LYS cc_start: 0.9302 (mmmt) cc_final: 0.9008 (mmmt) REVERT: Q 32 ILE cc_start: 0.9075 (mt) cc_final: 0.8779 (mt) REVERT: R 12 LEU cc_start: 0.9689 (tp) cc_final: 0.9359 (tp) REVERT: S 3 GLU cc_start: 0.8941 (mp0) cc_final: 0.8634 (mm-30) REVERT: T 29 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9222 (mmmt) REVERT: U 3 GLU cc_start: 0.9100 (mp0) cc_final: 0.8854 (mp0) REVERT: U 17 GLU cc_start: 0.9219 (mp0) cc_final: 0.8869 (mp0) REVERT: U 29 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8971 (mmmt) REVERT: Z 29 LYS cc_start: 0.9433 (mmpt) cc_final: 0.9171 (mmmt) REVERT: a 3 GLU cc_start: 0.9135 (mp0) cc_final: 0.8701 (mm-30) REVERT: e 3 GLU cc_start: 0.9187 (mp0) cc_final: 0.8597 (mm-30) REVERT: f 3 GLU cc_start: 0.8981 (mp0) cc_final: 0.8692 (mp0) REVERT: g 3 GLU cc_start: 0.9133 (mp0) cc_final: 0.8902 (mm-30) REVERT: h 29 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9194 (mmmt) REVERT: i 3 GLU cc_start: 0.9025 (mp0) cc_final: 0.8774 (mm-30) REVERT: j 29 LYS cc_start: 0.9414 (tptt) cc_final: 0.8780 (tmmt) REVERT: k 3 GLU cc_start: 0.8927 (mp0) cc_final: 0.8684 (mm-30) REVERT: l 19 LEU cc_start: 0.9129 (mt) cc_final: 0.8513 (tt) REVERT: l 29 LYS cc_start: 0.9393 (tptt) cc_final: 0.8979 (tmmt) REVERT: m 3 GLU cc_start: 0.8845 (pp20) cc_final: 0.8378 (mm-30) REVERT: n 29 LYS cc_start: 0.9367 (mmtt) cc_final: 0.8885 (tmmt) REVERT: o 3 GLU cc_start: 0.9046 (mp0) cc_final: 0.8709 (mm-30) outliers start: 1 outliers final: 1 residues processed: 478 average time/residue: 0.4064 time to fit residues: 238.6056 Evaluate side-chains 342 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- 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** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** T 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 ** 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: 0.8664 moved from start: 0.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11439 Z= 0.270 Angle : 0.891 7.580 15211 Z= 0.472 Chirality : 0.040 0.219 1927 Planarity : 0.003 0.037 1886 Dihedral : 5.479 44.238 1558 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.09 % Allowed : 0.90 % Favored : 99.01 % 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: 0.50 (0.21), residues: 1394 helix: 0.45 (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 L 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 474 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 1.483 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: A 3 GLU cc_start: 0.8982 (mp0) cc_final: 0.8688 (mp0) REVERT: B 29 LYS cc_start: 0.9398 (mmmt) cc_final: 0.8943 (mmmt) REVERT: B 32 ILE cc_start: 0.9209 (mt) cc_final: 0.8834 (mt) REVERT: C 3 GLU cc_start: 0.9015 (mp0) cc_final: 0.8558 (mm-30) REVERT: D 3 GLU cc_start: 0.9050 (mp0) cc_final: 0.8666 (mm-30) REVERT: D 24 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8712 (mm-30) REVERT: D 29 LYS cc_start: 0.9402 (mmpt) cc_final: 0.9201 (mmmt) REVERT: F 3 GLU cc_start: 0.9037 (mp0) cc_final: 0.8812 (mm-30) REVERT: F 29 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9235 (mmtp) REVERT: G 29 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9119 (mmmt) REVERT: I 29 LYS cc_start: 0.9514 (mmmt) cc_final: 0.9176 (tppt) REVERT: K 29 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9254 (mmmt) REVERT: L 3 GLU cc_start: 0.9045 (mp0) cc_final: 0.8714 (mm-30) REVERT: O 31 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8424 (mp0) REVERT: P 24 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8790 (mm-30) REVERT: Q 3 GLU cc_start: 0.9132 (mp0) cc_final: 0.8743 (mm-30) REVERT: R 12 LEU cc_start: 0.9665 (tp) cc_final: 0.9322 (tp) REVERT: S 3 GLU cc_start: 0.8962 (mp0) cc_final: 0.8640 (mm-30) REVERT: S 24 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8462 (mm-30) REVERT: T 29 LYS cc_start: 0.9487 (mmmt) cc_final: 0.9249 (mmtp) REVERT: U 3 GLU cc_start: 0.9098 (mp0) cc_final: 0.8836 (mp0) REVERT: U 17 GLU cc_start: 0.9085 (mp0) cc_final: 0.8694 (mp0) REVERT: U 27 LYS cc_start: 0.9252 (tmmt) cc_final: 0.8967 (ptmm) REVERT: Y 3 GLU cc_start: 0.9059 (mp0) cc_final: 0.8747 (mp0) REVERT: a 3 GLU cc_start: 0.9106 (mp0) cc_final: 0.8728 (mm-30) REVERT: d 3 GLU cc_start: 0.8999 (mp0) cc_final: 0.8697 (mm-30) REVERT: e 3 GLU cc_start: 0.9149 (mp0) cc_final: 0.8576 (mm-30) REVERT: f 8 GLU cc_start: 0.9160 (pm20) cc_final: 0.8952 (pm20) REVERT: g 3 GLU cc_start: 0.9130 (mp0) cc_final: 0.8890 (mm-30) REVERT: h 29 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9193 (mmtp) REVERT: i 3 GLU cc_start: 0.9023 (mp0) cc_final: 0.8759 (mm-30) REVERT: j 29 LYS cc_start: 0.9362 (tptt) cc_final: 0.8767 (tmmt) REVERT: k 3 GLU cc_start: 0.8970 (mp0) cc_final: 0.8748 (mm-30) REVERT: l 19 LEU cc_start: 0.9124 (mt) cc_final: 0.8468 (tt) REVERT: l 29 LYS cc_start: 0.9380 (tptt) cc_final: 0.8976 (tmmt) REVERT: m 3 GLU cc_start: 0.8817 (pp20) cc_final: 0.8443 (mm-30) REVERT: n 29 LYS cc_start: 0.9355 (mmtt) cc_final: 0.8856 (tmmt) REVERT: o 3 GLU cc_start: 0.9048 (mp0) cc_final: 0.8695 (mm-30) outliers start: 1 outliers final: 1 residues processed: 473 average time/residue: 0.4027 time to fit residues: 233.4534 Evaluate side-chains 381 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN B 36 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN T 36 GLN ** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.092810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.083707 restraints weight = 63534.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.084957 restraints weight = 35967.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.085756 restraints weight = 23525.243| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.004 0.051 11439 Z= 0.269 Angle : 0.869 8.843 15211 Z= 0.458 Chirality : 0.040 0.219 1927 Planarity : 0.003 0.035 1886 Dihedral : 5.477 46.468 1558 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.18 % Allowed : 1.45 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1394 helix: 0.53 (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 Y 6 =============================================================================== Job complete usr+sys time: 3934.52 seconds wall clock time: 70 minutes 41.21 seconds (4241.21 seconds total)