Starting phenix.real_space_refine
on Sun Mar 24 20:54:51 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/03_2024/8c96_16503.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/03_2024/8c96_16503.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/03_2024/8c96_16503.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/03_2024/8c96_16503.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/03_2024/8c96_16503.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/03_2024/8c96_16503.pdb"
  }
  resolution = 4.43
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
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=   0.003 sd=   0.073
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: 5
    Type Number    sf(0)   Gaussians
     P    1475      5.49       5
     S      35      5.16       5
     C   21970      2.51       5
     N    8289      2.21       5
     O   12445      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: 44214
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 31713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1475, 31713
          Classifications: {'RNA': 1475}
          Modifications used: {'rna2p_pur': 143, 'rna2p_pyr': 75, 'rna3p_pur': 728, 'rna3p_pyr': 529}
          Link IDs: {'rna2p': 218, 'rna3p': 1256}
          Chain breaks: 7
    Chain: "D"
      Number of atoms: 1306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1306
          Classifications: {'peptide': 175}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1438
          Classifications: {'peptide': 187}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 182}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1129
          Classifications: {'peptide': 142}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 135}
    Chain: "K"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 938
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 778
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 106}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 960
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "P"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 917
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "S"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 789
          Classifications: {'peptide': 101}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 99}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 509
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
    Chain: "0"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 444
          Classifications: {'peptide': 56}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 54}
    Chain: "2"
      Number of atoms: 312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 312
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
    Chain: "Z"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 439
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 2, 'TRANS': 54}
  Time building chain proxies: 21.32, per 1000 atoms: 0.48
  Number of scatterers: 44214
  At special positions: 0
  Unit cell: (148.75, 183.75, 206.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P    1475     15.00
     O   12445      8.00
     N    8289      7.00
     C   21970      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: 26.79
  Conformation dependent library (CDL) restraints added in 3.3 seconds
  

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2948

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 22 sheets defined
      33.5% alpha, 16.9% beta
      484 base pairs and 703 stacking pairs defined.
    Time for finding SS restraints: 23.74
  Creating SS restraints...
    Processing helix  chain 'D' and resid 61 through 72
      removed outlier: 3.512A  pdb=" N   HIS D  67 " --> pdb=" O   PRO D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 102
      removed outlier: 3.719A  pdb=" N   ALA D 102 " --> pdb=" O   GLU D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 125
    Processing helix  chain 'E' and resid 15 through 21
      removed outlier: 3.561A  pdb=" N   PHE E  19 " --> pdb=" O   SER E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 24 through 40
      removed outlier: 3.510A  pdb=" N   ARG E  40 " --> pdb=" O   ALA E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
    Processing helix  chain 'E' and resid 154 through 162
    Processing helix  chain 'E' and resid 176 through 183
    Processing helix  chain 'E' and resid 189 through 199
    Processing helix  chain 'J' and resid 24 through 38
    Processing helix  chain 'J' and resid 58 through 62
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 89 through 96
    Processing helix  chain 'J' and resid 96 through 109
      removed outlier: 3.902A  pdb=" N   VAL J 100 " --> pdb=" O   ARG J  96 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 121
      removed outlier: 3.574A  pdb=" N   LYS J 121 " --> pdb=" O   ALA J 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 113
      removed outlier: 4.128A  pdb=" N   MET K 113 " --> pdb=" O   GLU K 110 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 6
      removed outlier: 3.797A  pdb=" N   LEU L   6 " --> pdb=" O   LEU L   3 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 28 through 33
      removed outlier: 4.130A  pdb=" N   GLY L  31 " --> pdb=" O   GLY L  28 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY L  32 " --> pdb=" O   LYS L  29 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ARG L  33 " --> pdb=" O   THR L  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 28 through 33'
    Processing helix  chain 'L' and resid 70 through 74
    Processing helix  chain 'L' and resid 128 through 138
      removed outlier: 3.539A  pdb=" N   ALA L 133 " --> pdb=" O   LYS L 129 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 13 through 32
    Processing helix  chain 'N' and resid 37 through 55
      removed outlier: 3.845A  pdb=" N   GLU N  43 " --> pdb=" O   PRO N  39 " (cutoff:3.500A)
      Proline residue:  N  50  - end of helix
    Processing helix  chain 'N' and resid 59 through 69
    Processing helix  chain 'N' and resid 72 through 79
    Processing helix  chain 'N' and resid 82 through 87
    Processing helix  chain 'P' and resid 2 through 10
    Processing helix  chain 'P' and resid 52 through 55
    Processing helix  chain 'P' and resid 96 through 101
    Processing helix  chain 'Q' and resid 5 through 19
      removed outlier: 3.813A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 25 through 30
    Processing helix  chain 'Q' and resid 30 through 72
      removed outlier: 4.122A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ARG Q  50 " --> pdb=" O   TYR Q  46 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 74 through 85
    Processing helix  chain 'Q' and resid 90 through 101
      removed outlier: 3.754A  pdb=" N   VAL Q  99 " --> pdb=" O   ALA Q  95 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   PHE Q 100 " --> pdb=" O   ASP Q  96 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 102 through 117
      removed outlier: 4.252A  pdb=" N   ALA Q 117 " --> pdb=" O   LYS Q 113 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 15 through 22
      removed outlier: 3.886A  pdb=" N   LEU S  19 " --> pdb=" O   GLN S  15 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   VAL S  20 " --> pdb=" O   LYS S  16 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 4.001A  pdb=" N   ASP S  34 " --> pdb=" O   SER S  30 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 42 through 62
      removed outlier: 3.923A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 2 through 8
    Processing helix  chain 'Y' and resid 9 through 30
      removed outlier: 4.482A  pdb=" N   GLN Y  25 " --> pdb=" O   LEU Y  21 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 4.136A  pdb=" N   LYS Y  44 " --> pdb=" O   SER Y  40 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 8 through 16
    Processing helix  chain '0' and resid 17 through 20
      removed outlier: 4.183A  pdb=" N   ALA 0  20 " --> pdb=" O   SER 0  17 " (cutoff:3.500A)
      No H-bonds generated for 'chain '0' and resid 17 through 20'
    Processing helix  chain '2' and resid 8 through 17
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 3.946A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
    Processing helix  chain 'Z' and resid 16 through 27
    Processing helix  chain 'Z' and resid 40 through 50
    Processing sheet with id=AA1, first strand: chain 'D' and resid 108 through 111
      removed outlier: 6.733A  pdb=" N   LYS D   8 " --> pdb=" O   GLU D  28 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLU D  28 " --> pdb=" O   LYS D   8 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL D 189 " --> pdb=" O   THR D  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 79 through 83
      removed outlier: 6.306A  pdb=" N   ALA D  47 " --> pdb=" O   VAL D  37 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   VAL D  37 " --> pdb=" O   ALA D  47 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   GLN D  49 " --> pdb=" O   THR D  35 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR D  35 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN D  32 " --> pdb=" O   ILE D  96 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE D  96 " --> pdb=" O   ASN D  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 116 through 119
      removed outlier: 3.985A  pdb=" N   MET D 165 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   PHE D 118 " --> pdb=" O   GLY D 163 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   GLY D 163 " --> pdb=" O   PHE D 118 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 2 through 4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 120
      removed outlier: 3.517A  pdb=" N   ILE E 119 " --> pdb=" O   VAL E 186 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   MET E 188 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   LEU E 147 " --> pdb=" O   VAL E 187 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ARG E 170 " --> pdb=" O   ILE E 148 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'J' and resid 122 through 124
      removed outlier: 6.590A  pdb=" N   TRP J  15 " --> pdb=" O   GLN J 138 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 73 through 74
    Processing sheet with id=AA8, first strand: chain 'K' and resid 7 through 10
      removed outlier: 7.099A  pdb=" N   LYS K  40 " --> pdb=" O   ILE K  22 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   VAL K  24 " --> pdb=" O   ILE K  38 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   ILE K  38 " --> pdb=" O   VAL K  24 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE K  41 " --> pdb=" O   LEU K  58 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU K  58 " --> pdb=" O   ILE K  41 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ALA K  83 " --> pdb=" O   VAL K  63 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   CYS K  84 " --> pdb=" O   MET K   7 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   ASN K   9 " --> pdb=" O   CYS K  84 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   LEU K  86 " --> pdb=" O   ASN K   9 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 69 through 70
      removed outlier: 4.584A  pdb=" N   VAL K  76 " --> pdb=" O   VAL P  72 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL P  72 " --> pdb=" O   VAL K  76 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG K  78 " --> pdb=" O   GLU P  70 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ALA P  57 " --> pdb=" O   ILE P  49 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   ILE P  49 " --> pdb=" O   ALA P  57 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   THR P  59 " --> pdb=" O   ILE P  47 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   ILE P  63 " --> pdb=" O   GLU P  43 " (cutoff:3.500A)
      removed outlier: 8.864A  pdb=" N   GLU P  43 " --> pdb=" O   ILE P  63 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   SER P  82 " --> pdb=" O   LYS P  28 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   TRP P  30 " --> pdb=" O   VAL P  80 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   VAL P  80 " --> pdb=" O   TRP P  30 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 122 through 123
      removed outlier: 5.554A  pdb=" N   VAL L 122 " --> pdb=" O   GLU L 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'N' and resid 33 through 36
      removed outlier: 4.588A  pdb=" N   MET N 110 " --> pdb=" O   CYS N 100 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 11 through 14
      removed outlier: 3.591A  pdb=" N   VAL R   4 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET R  40 " --> pdb=" O   VAL R   4 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 20 through 22
      removed outlier: 3.752A  pdb=" N   ALA R  65 " --> pdb=" O   ASP R  95 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   LYS R  97 " --> pdb=" O   VAL R  63 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   VAL R  63 " --> pdb=" O   LYS R  97 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   THR R  99 " --> pdb=" O   ALA R  61 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   ALA R  61 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   ILE R 101 " --> pdb=" O   ILE R  59 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   ILE R  59 " --> pdb=" O   ILE R 101 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 72 through 77
    Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 10
      removed outlier: 3.723A  pdb=" N   ILE S 103 " --> pdb=" O   HIS S   7 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   HIS S   9 " --> pdb=" O   SER S 101 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   SER S 101 " --> pdb=" O   HIS S   9 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 82 through 84
    Processing sheet with id=AB8, first strand: chain 'U' and resid 63 through 65
      removed outlier: 6.551A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   GLU U   9 " --> pdb=" O   PHE U  72 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ASN U  73 " --> pdb=" O   LYS U  78 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LYS U  78 " --> pdb=" O   ASN U  73 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'U' and resid 40 through 41
      removed outlier: 3.992A  pdb=" N   VAL U  41 " --> pdb=" O   LYS U  60 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LYS U  60 " --> pdb=" O   VAL U  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'U' and resid 82 through 86
    Processing sheet with id=AC2, first strand: chain '0' and resid 27 through 29
    Processing sheet with id=AC3, first strand: chain '0' and resid 47 through 48
    Processing sheet with id=AC4, first strand: chain 'Z' and resid 35 through 37
      removed outlier: 3.848A  pdb=" N   VAL Z  35 " --> pdb=" O   ILE Z   6 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE Z   6 " --> pdb=" O   VAL Z  35 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   ARG Z  37 " --> pdb=" O   ILE Z   4 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ILE Z   4 " --> pdb=" O   ARG Z  37 " (cutoff:3.500A)

    457 hydrogen bonds defined for protein.
    1290 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1236 hydrogen bonds
      2006 hydrogen bond angles
      0 basepair planarities
      484 basepair parallelities
      703 stacking parallelities
  Total time for adding SS restraints: 41.19

  Time building geometry restraints manager: 28.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 7165
        1.33 -     1.45: 20009
        1.45 -     1.57: 17983
        1.57 -     1.69: 2943
        1.69 -     1.81: 67
  Bond restraints: 48167
  Sorted by residual:
  bond pdb=" C1'   U A 827 "
       pdb=" N1    U A 827 "
    ideal  model  delta    sigma   weight residual
    1.480  1.574 -0.094 1.50e-02 4.44e+03 3.90e+01
  bond pdb=" N   MET R   1 "
       pdb=" CA  MET R   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.13e+00
  bond pdb=" N   MET Y   1 "
       pdb=" CA  MET Y   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.11e+00
  bond pdb=" N   ALA U   1 "
       pdb=" CA  ALA U   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.07e+00
  bond pdb=" N   ALA Q   1 "
       pdb=" CA  ALA Q   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  ... (remaining 48162 not shown)

  Histogram of bond angle deviations from ideal:
      100.31 -   107.04: 8970
      107.04 -   113.77: 29645
      113.77 -   120.51: 17442
      120.51 -   127.24: 12950
      127.24 -   133.97: 3343
  Bond angle restraints: 72350
  Sorted by residual:
  angle pdb=" C3'   G A 271 "
        pdb=" O3'   G A 271 "
        pdb=" P     A A 272 "
      ideal   model   delta    sigma   weight residual
     120.20  123.80   -3.60 1.50e+00 4.44e-01 5.75e+00
  angle pdb=" C4'   G A 271 "
        pdb=" C3'   G A 271 "
        pdb=" O3'   G A 271 "
      ideal   model   delta    sigma   weight residual
     109.40  112.92   -3.52 1.50e+00 4.44e-01 5.52e+00
  angle pdb=" C   HIS N  31 "
        pdb=" N   GLU N  32 "
        pdb=" CA  GLU N  32 "
      ideal   model   delta    sigma   weight residual
     121.54  125.82   -4.28 1.91e+00 2.74e-01 5.01e+00
  angle pdb=" C2'   A A1287 "
        pdb=" C1'   A A1287 "
        pdb=" N9    A A1287 "
      ideal   model   delta    sigma   weight residual
     112.00  115.09   -3.09 1.50e+00 4.44e-01 4.23e+00
  angle pdb=" N   LYS D  62 "
        pdb=" CA  LYS D  62 "
        pdb=" C   LYS D  62 "
      ideal   model   delta    sigma   weight residual
     109.81  114.30   -4.49 2.21e+00 2.05e-01 4.13e+00
  ... (remaining 72345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.99: 27055
       34.99 -    69.98: 3291
       69.98 -   104.96: 388
      104.96 -   139.95: 15
      139.95 -   174.94: 4
  Dihedral angle restraints: 30753
    sinusoidal: 26192
      harmonic: 4561
  Sorted by residual:
  dihedral pdb=" O4'   U A 828 "
           pdb=" C1'   U A 828 "
           pdb=" N1    U A 828 "
           pdb=" C2    U A 828 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   45.69 -173.69     1      1.70e+01 3.46e-03 6.62e+01
  dihedral pdb=" O4'   C A 323 "
           pdb=" C1'   C A 323 "
           pdb=" N1    C A 323 "
           pdb=" C2    C A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -12.02 -115.98     1      1.70e+01 3.46e-03 4.78e+01
  dihedral pdb=" C4'   U A 828 "
           pdb=" C3'   U A 828 "
           pdb=" O3'   U A 828 "
           pdb=" P     A A 829 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   64.94 -174.94     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 30750 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 7389
       0.031 -    0.062: 1624
       0.062 -    0.093: 149
       0.093 -    0.124: 144
       0.124 -    0.154: 12
  Chirality restraints: 9318
  Sorted by residual:
  chirality pdb=" C1'   U A 827 "
            pdb=" O4'   U A 827 "
            pdb=" C2'   U A 827 "
            pdb=" N1    U A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  ILE N  33 "
            pdb=" N   ILE N  33 "
            pdb=" C   ILE N  33 "
            pdb=" CB  ILE N  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  chirality pdb=" CA  ILE R  74 "
            pdb=" N   ILE R  74 "
            pdb=" C   ILE R  74 "
            pdb=" CB  ILE R  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 9315 not shown)

  Planarity restraints: 3647
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 259 "    0.010 2.00e-02 2.50e+03   1.32e-02 5.22e+00
        pdb=" N9    G A 259 "   -0.008 2.00e-02 2.50e+03
        pdb=" C8    G A 259 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G A 259 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    G A 259 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 259 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G A 259 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    G A 259 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G A 259 "   -0.035 2.00e-02 2.50e+03
        pdb=" N2    G A 259 "    0.026 2.00e-02 2.50e+03
        pdb=" N3    G A 259 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G A 259 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 175 "    0.012 2.00e-02 2.50e+03   1.19e-02 4.28e+00
        pdb=" N9    G A 175 "   -0.014 2.00e-02 2.50e+03
        pdb=" C8    G A 175 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G A 175 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G A 175 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 175 "    0.030 2.00e-02 2.50e+03
        pdb=" O6    G A 175 "   -0.017 2.00e-02 2.50e+03
        pdb=" N1    G A 175 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G A 175 "    0.007 2.00e-02 2.50e+03
        pdb=" N2    G A 175 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    G A 175 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G A 175 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 269 "    0.006 2.00e-02 2.50e+03   1.25e-02 3.53e+00
        pdb=" N1    C A 269 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2    C A 269 "    0.028 2.00e-02 2.50e+03
        pdb=" O2    C A 269 "   -0.018 2.00e-02 2.50e+03
        pdb=" N3    C A 269 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    C A 269 "    0.010 2.00e-02 2.50e+03
        pdb=" N4    C A 269 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    C A 269 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    C A 269 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 3644 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 392
        2.52 -     3.12: 32713
        3.12 -     3.71: 84293
        3.71 -     4.31: 115317
        4.31 -     4.90: 159244
  Nonbonded interactions: 391959
  Sorted by model distance:
  nonbonded pdb=" O2'   A A1009 "
            pdb=" O4'   A A1010 "
     model   vdw
     1.928 2.440
  nonbonded pdb=" O2'   A A2632 "
            pdb=" O2'   G A2811 "
     model   vdw
     1.941 2.440
  nonbonded pdb=" O2'   G A 214 "
            pdb=" O4'   G A 215 "
     model   vdw
     1.949 2.440
  nonbonded pdb=" OP2   G A 117 "
            pdb=" O2'   A A 119 "
     model   vdw
     1.957 2.440
  nonbonded pdb=" O2'   G A 261 "
            pdb=" O2'   C A 610 "
     model   vdw
     1.972 2.440
  ... (remaining 391954 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.380
  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:             0.040
  Extract box with map and model:          8.150
  Check model and map are aligned:         0.590
  Set scattering table:                    0.350
  Process input model:                     156.030
  Find NCS groups from input model:        0.870
  Set up NCS constraints:                  0.110
  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:             0.010
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  171.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
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      :  0.001   0.094  48167  Z= 0.090
  Angle     :  0.364   5.780  72350  Z= 0.188
  Chirality :  0.026   0.154   9318
  Planarity :  0.002   0.029   3647
  Dihedral  : 22.541 174.940  27805
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.82 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.44 %
    Favored  : 96.48 %
  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:  0.57 (0.22), residues: 1569
  helix:  2.09 (0.25), residues: 474
  sheet:  0.52 (0.33), residues: 241
  loop : -0.66 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R  92 
 HIS   0.002   0.000   HIS S 102 
 PHE   0.006   0.001   PHE Z  52 
 TYR   0.008   0.001   TYR N 112 
 ARG   0.004   0.000   ARG 0  12 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 311
  time to evaluate  : 2.575 
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: D   11 MET cc_start: 0.6948 (ppp) cc_final: 0.6433 (tmm)
REVERT: D   18 ASP cc_start: 0.8531 (m-30) cc_final: 0.8215 (t0)
REVERT: E   41 GLN cc_start: 0.8815 (tp40) cc_final: 0.8479 (tm-30)
REVERT: E  115 GLN cc_start: 0.9040 (tp40) cc_final: 0.8691 (tm-30)
REVERT: J   53 TYR cc_start: 0.8045 (m-10) cc_final: 0.7412 (m-80)
REVERT: J   92 MET cc_start: 0.9379 (ttm) cc_final: 0.9092 (tpt)
REVERT: J  105 VAL cc_start: 0.9319 (t) cc_final: 0.9010 (p)
REVERT: K   58 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6037 (pt)
REVERT: K   79 PHE cc_start: 0.9327 (m-80) cc_final: 0.8653 (m-80)
REVERT: K   87 LEU cc_start: 0.7049 (mt) cc_final: 0.6364 (mp)
REVERT: N   13 ASN cc_start: 0.9175 (m-40) cc_final: 0.8861 (m-40)
REVERT: N  107 ASN cc_start: 0.8989 (t0) cc_final: 0.8738 (t0)
REVERT: P    2 ASN cc_start: 0.9229 (m-40) cc_final: 0.9025 (m-40)
REVERT: P   73 PHE cc_start: 0.7594 (m-80) cc_final: 0.7124 (m-80)
REVERT: Q   36 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8419 (tm-30)
REVERT: Q   48 ASP cc_start: 0.7633 (t0) cc_final: 0.6993 (t0)
REVERT: R   86 GLN cc_start: 0.7765 (pp30) cc_final: 0.7457 (pp30)
REVERT: R   87 GLN cc_start: 0.7827 (pp30) cc_final: 0.7146 (pp30)
REVERT: S   49 LYS cc_start: 0.9570 (tptt) cc_final: 0.8957 (tptt)
REVERT: S   68 ASP cc_start: 0.8130 (p0) cc_final: 0.7548 (p0)
REVERT: S   74 ILE cc_start: 0.9276 (tt) cc_final: 0.8851 (pt)
REVERT: S   99 ARG cc_start: 0.7696 (mpt180) cc_final: 0.6970 (mpt180)
REVERT: Y    1 MET cc_start: 0.7729 (ppp) cc_final: 0.7028 (ppp)
REVERT: Y    7 ARG cc_start: 0.8404 (ptt180) cc_final: 0.7890 (ptt180)
REVERT: Y   29 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.7586 (ptt-90)
REVERT: Y   30 MET cc_start: 0.8790 (mmp) cc_final: 0.8427 (mmm)
REVERT: 0   14 MET cc_start: 0.9038 (mpp) cc_final: 0.8833 (mpp)
REVERT: Z   20 LYS cc_start: 0.9309 (tptm) cc_final: 0.8834 (tptp)
REVERT: Z   24 LEU cc_start: 0.9538 (pp) cc_final: 0.9193 (pp)
REVERT: Z   43 ILE cc_start: 0.8565 (mm) cc_final: 0.8129 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 311
  average time/residue: 0.6055
  time to fit residues: 301.0032
Evaluate side-chains
  192 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 2.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 254 optimal weight:    9.9990
   chunk 228 optimal weight:   20.0000
   chunk 126 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 153 optimal weight:    6.9990
   chunk 121 optimal weight:   10.0000
   chunk 235 optimal weight:   20.0000
   chunk 91 optimal weight:   10.0000
   chunk 143 optimal weight:   20.0000
   chunk 175 optimal weight:    0.0570
   chunk 273 optimal weight:    9.9990
   overall best weight:    7.4108

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 HIS
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 164 GLN
D 173 GLN
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 132 HIS
J 136 GLN
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  57 ASN
Y  15 ASN
Y  25 GLN
** 2  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  48167  Z= 0.301
  Angle     :  0.694   9.789  72350  Z= 0.348
  Chirality :  0.035   0.225   9318
  Planarity :  0.005   0.057   3647
  Dihedral  : 24.019 178.594  24691
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 28.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.90 %
    Favored  : 96.02 %
  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: -0.43 (0.20), residues: 1569
  helix:  0.88 (0.23), residues: 483
  sheet: -0.08 (0.32), residues: 243
  loop : -1.04 (0.20), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP E  78 
 HIS   0.011   0.002   HIS N   3 
 PHE   0.023   0.002   PHE N  21 
 TYR   0.016   0.002   TYR J  53 
 ARG   0.014   0.001   ARG J  37 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 2.236 
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: E   19 PHE cc_start: 0.8051 (m-80) cc_final: 0.7832 (m-80)
REVERT: E  188 MET cc_start: 0.9035 (ptm) cc_final: 0.8756 (ptm)
REVERT: J   46 PRO cc_start: 0.9544 (Cg_endo) cc_final: 0.9296 (Cg_exo)
REVERT: J   53 TYR cc_start: 0.8708 (m-80) cc_final: 0.8062 (m-80)
REVERT: J   67 ASN cc_start: 0.8185 (t0) cc_final: 0.7627 (t0)
REVERT: J   92 MET cc_start: 0.9537 (ttm) cc_final: 0.9127 (tpt)
REVERT: K    3 GLN cc_start: 0.5911 (pm20) cc_final: 0.5630 (pm20)
REVERT: K    7 MET cc_start: 0.7761 (tpt) cc_final: 0.7424 (tmm)
REVERT: K   58 LEU cc_start: 0.6958 (tp) cc_final: 0.6581 (tp)
REVERT: K   79 PHE cc_start: 0.9322 (m-80) cc_final: 0.8830 (m-10)
REVERT: N    1 MET cc_start: 0.7624 (tpp) cc_final: 0.6923 (tmm)
REVERT: N   13 ASN cc_start: 0.9152 (m-40) cc_final: 0.8889 (m-40)
REVERT: N   20 MET cc_start: 0.9067 (ttm) cc_final: 0.8415 (tmm)
REVERT: N   21 PHE cc_start: 0.9182 (m-80) cc_final: 0.8749 (m-80)
REVERT: N   28 LEU cc_start: 0.9481 (tt) cc_final: 0.9235 (tp)
REVERT: P   58 PHE cc_start: 0.9259 (p90) cc_final: 0.8997 (p90)
REVERT: Q   30 VAL cc_start: 0.8891 (t) cc_final: 0.8481 (p)
REVERT: Q   36 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: Q   48 ASP cc_start: 0.8223 (t0) cc_final: 0.7547 (t0)
REVERT: R   85 LYS cc_start: 0.9368 (tttp) cc_final: 0.9051 (tttp)
REVERT: S   49 LYS cc_start: 0.9641 (tptt) cc_final: 0.9027 (tptt)
REVERT: S   68 ASP cc_start: 0.7980 (p0) cc_final: 0.7583 (p0)
REVERT: S   74 ILE cc_start: 0.9273 (tt) cc_final: 0.8846 (pt)
REVERT: S   99 ARG cc_start: 0.8125 (mpt180) cc_final: 0.7493 (mpt180)
REVERT: S  103 ILE cc_start: 0.9607 (pt) cc_final: 0.9363 (mp)
REVERT: Y    1 MET cc_start: 0.7952 (ppp) cc_final: 0.7129 (ppp)
REVERT: Y    7 ARG cc_start: 0.8418 (ptt180) cc_final: 0.8100 (ptt180)
REVERT: Y   29 ARG cc_start: 0.8235 (ptt-90) cc_final: 0.7730 (ptt-90)
REVERT: Y   30 MET cc_start: 0.8966 (mmp) cc_final: 0.8749 (mmm)
REVERT: 0    6 LYS cc_start: 0.8892 (tttt) cc_final: 0.8044 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9138 (mmmm)
REVERT: Z   20 LYS cc_start: 0.9370 (tptm) cc_final: 0.8976 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 236
  average time/residue: 0.5610
  time to fit residues: 218.5573
Evaluate side-chains
  181 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 2.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 151 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 227 optimal weight:   30.0000
   chunk 186 optimal weight:   10.0000
   chunk 75 optimal weight:   50.0000
   chunk 273 optimal weight:    0.9980
   chunk 295 optimal weight:    5.9990
   chunk 243 optimal weight:   20.0000
   chunk 271 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 219 optimal weight:   10.0000
   overall best weight:    5.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 GLN
J  58 ASN
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 107 ASN
** P   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
** 2  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  48167  Z= 0.219
  Angle     :  0.547   9.415  72350  Z= 0.278
  Chirality :  0.031   0.217   9318
  Planarity :  0.004   0.070   3647
  Dihedral  : 24.018 179.498  24691
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 21.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.74 %
    Favored  : 95.11 %
  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: -0.60 (0.20), residues: 1569
  helix:  0.86 (0.23), residues: 483
  sheet: -0.53 (0.30), residues: 267
  loop : -1.12 (0.20), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  78 
 HIS   0.006   0.001   HIS E  92 
 PHE   0.023   0.002   PHE N  21 
 TYR   0.008   0.002   TYR J  53 
 ARG   0.012   0.001   ARG Y  23 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 218
  time to evaluate  : 2.185 
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: E  188 MET cc_start: 0.8818 (ptm) cc_final: 0.8558 (ptm)
REVERT: J   53 TYR cc_start: 0.8705 (m-80) cc_final: 0.7579 (m-80)
REVERT: J   67 ASN cc_start: 0.8584 (t0) cc_final: 0.8012 (t0)
REVERT: J   92 MET cc_start: 0.9617 (ttm) cc_final: 0.9157 (tpp)
REVERT: K    1 MET cc_start: 0.6283 (tmm) cc_final: 0.4961 (tmm)
REVERT: K    7 MET cc_start: 0.7671 (tpt) cc_final: 0.7118 (tmm)
REVERT: K   58 LEU cc_start: 0.6740 (tp) cc_final: 0.6294 (tp)
REVERT: K   79 PHE cc_start: 0.9303 (m-80) cc_final: 0.8867 (m-80)
REVERT: K  110 GLU cc_start: 0.5335 (mp0) cc_final: 0.5124 (mp0)
REVERT: N   13 ASN cc_start: 0.9157 (m-40) cc_final: 0.8945 (m-40)
REVERT: N   20 MET cc_start: 0.9159 (ttm) cc_final: 0.8600 (tmm)
REVERT: N   21 PHE cc_start: 0.9302 (m-80) cc_final: 0.8844 (m-80)
REVERT: P    9 GLN cc_start: 0.8513 (mp-120) cc_final: 0.8308 (mm-40)
REVERT: P   58 PHE cc_start: 0.9072 (p90) cc_final: 0.8753 (p90)
REVERT: Q   21 LYS cc_start: 0.9402 (mmtt) cc_final: 0.9113 (pttt)
REVERT: Q   48 ASP cc_start: 0.8364 (t0) cc_final: 0.7717 (t0)
REVERT: R   70 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7759 (tm-30)
REVERT: R   85 LYS cc_start: 0.9367 (tttp) cc_final: 0.9126 (tptp)
REVERT: R   87 GLN cc_start: 0.8632 (pp30) cc_final: 0.8192 (pp30)
REVERT: S   49 LYS cc_start: 0.9628 (tptt) cc_final: 0.9292 (tptm)
REVERT: S   68 ASP cc_start: 0.8087 (p0) cc_final: 0.7542 (p0)
REVERT: S   74 ILE cc_start: 0.9315 (tt) cc_final: 0.9022 (mm)
REVERT: Y   18 LEU cc_start: 0.8845 (pp) cc_final: 0.8641 (tp)
REVERT: Y   29 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7723 (ptt-90)
REVERT: Y   30 MET cc_start: 0.9000 (mmp) cc_final: 0.8753 (mmm)
REVERT: 0    6 LYS cc_start: 0.8839 (tttt) cc_final: 0.7913 (tmtt)
REVERT: Z   20 LYS cc_start: 0.9357 (tptm) cc_final: 0.8971 (tptp)
REVERT: Z   51 SER cc_start: 0.9178 (p) cc_final: 0.8808 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 220
  average time/residue: 0.5331
  time to fit residues: 195.3844
Evaluate side-chains
  171 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 2.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 270 optimal weight:    0.6980
   chunk 205 optimal weight:   50.0000
   chunk 142 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   chunk 130 optimal weight:   30.0000
   chunk 183 optimal weight:    6.9990
   chunk 274 optimal weight:   20.0000
   chunk 290 optimal weight:    7.9990
   chunk 143 optimal weight:    8.9990
   chunk 260 optimal weight:   20.0000
   chunk 78 optimal weight:   20.0000
   overall best weight:    6.9390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 135 GLN
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 107 ASN
P  65 ASN
U  52 ASN
** 2  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.5398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  48167  Z= 0.282
  Angle     :  0.649   8.669  72350  Z= 0.328
  Chirality :  0.035   0.231   9318
  Planarity :  0.005   0.060   3647
  Dihedral  : 24.344 179.807  24691
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 31.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.82 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.51 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.20), residues: 1569
  helix:  0.47 (0.23), residues: 481
  sheet: -0.72 (0.30), residues: 269
  loop : -1.26 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP J  15 
 HIS   0.008   0.002   HIS N   3 
 PHE   0.021   0.002   PHE N  21 
 TYR   0.021   0.002   TYR K  32 
 ARG   0.012   0.001   ARG U  21 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 2.325 
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: E  188 MET cc_start: 0.8805 (ptm) cc_final: 0.8424 (ptm)
REVERT: J   53 TYR cc_start: 0.8657 (m-80) cc_final: 0.7767 (m-80)
REVERT: J   67 ASN cc_start: 0.8635 (t0) cc_final: 0.8103 (t0)
REVERT: J   92 MET cc_start: 0.9631 (ttm) cc_final: 0.9087 (tpp)
REVERT: K    1 MET cc_start: 0.6453 (tmm) cc_final: 0.4788 (pmm)
REVERT: K    7 MET cc_start: 0.7987 (tpt) cc_final: 0.7737 (tmm)
REVERT: K   58 LEU cc_start: 0.6714 (tp) cc_final: 0.6379 (tp)
REVERT: K   79 PHE cc_start: 0.9276 (m-80) cc_final: 0.8896 (m-10)
REVERT: L   81 ASP cc_start: 0.7611 (t70) cc_final: 0.6572 (m-30)
REVERT: N   10 LEU cc_start: 0.9350 (mp) cc_final: 0.9140 (mp)
REVERT: N   20 MET cc_start: 0.9230 (ttm) cc_final: 0.8913 (mtt)
REVERT: P   58 PHE cc_start: 0.8914 (p90) cc_final: 0.8576 (p90)
REVERT: Q   21 LYS cc_start: 0.9490 (mmtt) cc_final: 0.9129 (pttt)
REVERT: R   70 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: R   83 TYR cc_start: 0.7704 (t80) cc_final: 0.6838 (t80)
REVERT: S   49 LYS cc_start: 0.9615 (tptt) cc_final: 0.9343 (tptm)
REVERT: S   74 ILE cc_start: 0.9326 (tt) cc_final: 0.8915 (pt)
REVERT: Y   29 ARG cc_start: 0.8507 (ptt-90) cc_final: 0.7919 (ptt-90)
REVERT: Y   30 MET cc_start: 0.9109 (mmp) cc_final: 0.8831 (mmm)
REVERT: 0    6 LYS cc_start: 0.8902 (tttt) cc_final: 0.7996 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9469 (mmmm) cc_final: 0.9170 (mmmm)
REVERT: 0   14 MET cc_start: 0.9188 (mpp) cc_final: 0.8920 (mpp)
REVERT: Z   20 LYS cc_start: 0.9409 (tptm) cc_final: 0.8911 (tptp)
  outliers start: 1
  outliers final: 0
  residues processed: 221
  average time/residue: 0.5906
  time to fit residues: 215.2396
Evaluate side-chains
  167 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 2.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 242 optimal weight:    9.9990
   chunk 165 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 216 optimal weight:   30.0000
   chunk 120 optimal weight:   20.0000
   chunk 248 optimal weight:    6.9990
   chunk 201 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 148 optimal weight:    5.9990
   chunk 261 optimal weight:    6.9990
   chunk 73 optimal weight:   20.0000
   overall best weight:    7.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  29 HIS
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 HIS
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
2  13 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.6196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  48167  Z= 0.297
  Angle     :  0.657   9.472  72350  Z= 0.332
  Chirality :  0.036   0.236   9318
  Planarity :  0.005   0.062   3647
  Dihedral  : 24.515 179.456  24691
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 32.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  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: -1.28 (0.20), residues: 1569
  helix:  0.27 (0.23), residues: 479
  sheet: -1.17 (0.28), residues: 277
  loop : -1.40 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP R  92 
 HIS   0.007   0.002   HIS R  66 
 PHE   0.028   0.002   PHE E  19 
 TYR   0.014   0.002   TYR R  83 
 ARG   0.012   0.001   ARG R  79 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 2.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7964 (ppp) cc_final: 0.7642 (ppp)
REVERT: J   53 TYR cc_start: 0.9039 (m-80) cc_final: 0.8037 (m-80)
REVERT: J   67 ASN cc_start: 0.8506 (t0) cc_final: 0.8026 (t0)
REVERT: J   92 MET cc_start: 0.9656 (ttm) cc_final: 0.9139 (tpp)
REVERT: J  114 LEU cc_start: 0.8932 (mp) cc_final: 0.8398 (mp)
REVERT: K    1 MET cc_start: 0.5642 (tmm) cc_final: 0.4656 (pmm)
REVERT: K   58 LEU cc_start: 0.6543 (tp) cc_final: 0.6180 (tp)
REVERT: K   79 PHE cc_start: 0.9312 (m-80) cc_final: 0.8925 (m-10)
REVERT: L   81 ASP cc_start: 0.8158 (t70) cc_final: 0.6896 (m-30)
REVERT: N   13 ASN cc_start: 0.8982 (t0) cc_final: 0.8655 (t0)
REVERT: N   15 SER cc_start: 0.9440 (m) cc_final: 0.9189 (m)
REVERT: N   20 MET cc_start: 0.9239 (ttm) cc_final: 0.8618 (tmm)
REVERT: N   21 PHE cc_start: 0.9167 (m-10) cc_final: 0.8642 (m-80)
REVERT: P   12 MET cc_start: 0.9173 (mmt) cc_final: 0.7895 (mmm)
REVERT: P   58 PHE cc_start: 0.8936 (p90) cc_final: 0.8520 (p90)
REVERT: P   84 SER cc_start: 0.7206 (p) cc_final: 0.6878 (p)
REVERT: Q   21 LYS cc_start: 0.9487 (mmtt) cc_final: 0.9159 (pttt)
REVERT: Q   55 GLN cc_start: 0.9149 (mp10) cc_final: 0.8880 (mp10)
REVERT: R   70 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7708 (tm-30)
REVERT: R   85 LYS cc_start: 0.9482 (tmtt) cc_final: 0.9238 (tptp)
REVERT: S   49 LYS cc_start: 0.9634 (tptt) cc_final: 0.9425 (tptt)
REVERT: S   68 ASP cc_start: 0.8017 (p0) cc_final: 0.7587 (p0)
REVERT: S   74 ILE cc_start: 0.9345 (tt) cc_final: 0.8914 (pt)
REVERT: U    9 GLU cc_start: 0.8263 (tt0) cc_final: 0.7937 (tt0)
REVERT: Y    1 MET cc_start: 0.8338 (ppp) cc_final: 0.8045 (ppp)
REVERT: Y    7 ARG cc_start: 0.8764 (ptt180) cc_final: 0.8243 (ptt180)
REVERT: Y   29 ARG cc_start: 0.8458 (ptt-90) cc_final: 0.7510 (ptt-90)
REVERT: Y   30 MET cc_start: 0.9121 (mmp) cc_final: 0.8899 (mmp)
REVERT: 0    6 LYS cc_start: 0.8834 (tttt) cc_final: 0.7963 (tmtt)
REVERT: 0   14 MET cc_start: 0.9252 (mpp) cc_final: 0.8956 (mpp)
REVERT: 0   19 ASP cc_start: 0.8761 (m-30) cc_final: 0.8458 (m-30)
REVERT: Z   20 LYS cc_start: 0.9409 (tptm) cc_final: 0.9016 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.5734
  time to fit residues: 191.7387
Evaluate side-chains
  171 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 2.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 262 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 170 optimal weight:   20.0000
   chunk 71 optimal weight:   20.0000
   chunk 291 optimal weight:    4.9990
   chunk 241 optimal weight:    7.9990
   chunk 134 optimal weight:   20.0000
   chunk 24 optimal weight:   30.0000
   chunk 96 optimal weight:   10.0000
   chunk 152 optimal weight:    5.9990
   overall best weight:    6.9992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  89 ASN
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  80 ASN
R  18 GLN
** U  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
2  13 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.6596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  48167  Z= 0.270
  Angle     :  0.636   9.575  72350  Z= 0.321
  Chirality :  0.035   0.262   9318
  Planarity :  0.005   0.071   3647
  Dihedral  : 24.519 178.638  24691
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 31.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.36 %
    Favored  : 96.56 %
  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: -1.33 (0.20), residues: 1569
  helix:  0.35 (0.23), residues: 474
  sheet: -1.22 (0.28), residues: 287
  loop : -1.50 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP P  30 
 HIS   0.007   0.002   HIS U  44 
 PHE   0.012   0.002   PHE N  80 
 TYR   0.011   0.002   TYR N 112 
 ARG   0.009   0.001   ARG R  79 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 2.348 
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: E   19 PHE cc_start: 0.8201 (m-80) cc_final: 0.7901 (m-80)
REVERT: J   53 TYR cc_start: 0.8982 (m-80) cc_final: 0.7815 (m-80)
REVERT: J   67 ASN cc_start: 0.8670 (t0) cc_final: 0.8193 (t0)
REVERT: J   71 ASP cc_start: 0.8319 (m-30) cc_final: 0.7837 (m-30)
REVERT: J   92 MET cc_start: 0.9652 (ttm) cc_final: 0.9117 (tpp)
REVERT: J  108 MET cc_start: 0.8301 (tpt) cc_final: 0.7968 (mmm)
REVERT: K   79 PHE cc_start: 0.9298 (m-80) cc_final: 0.8888 (m-80)
REVERT: N   10 LEU cc_start: 0.9280 (mp) cc_final: 0.9079 (mp)
REVERT: N   13 ASN cc_start: 0.8999 (t0) cc_final: 0.8708 (t0)
REVERT: N   20 MET cc_start: 0.9254 (ttm) cc_final: 0.8953 (mtt)
REVERT: N  110 MET cc_start: 0.8496 (mpp) cc_final: 0.8275 (mpp)
REVERT: P   58 PHE cc_start: 0.8945 (p90) cc_final: 0.8503 (p90)
REVERT: P   70 GLU cc_start: 0.7031 (pm20) cc_final: 0.6819 (pm20)
REVERT: Q   21 LYS cc_start: 0.9499 (mmtt) cc_final: 0.9200 (mmmt)
REVERT: Q   48 ASP cc_start: 0.8527 (t0) cc_final: 0.7903 (t0)
REVERT: R   18 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7595 (pm20)
REVERT: R   83 TYR cc_start: 0.7808 (t80) cc_final: 0.7116 (t80)
REVERT: S   49 LYS cc_start: 0.9655 (tptt) cc_final: 0.8910 (tptm)
REVERT: S   68 ASP cc_start: 0.7744 (p0) cc_final: 0.7367 (p0)
REVERT: S   74 ILE cc_start: 0.9355 (tt) cc_final: 0.8944 (pt)
REVERT: S   82 MET cc_start: 0.7185 (tpp) cc_final: 0.6908 (tpp)
REVERT: U    9 GLU cc_start: 0.8229 (tt0) cc_final: 0.7613 (tt0)
REVERT: Y    7 ARG cc_start: 0.8773 (ptt180) cc_final: 0.8262 (ptt180)
REVERT: Y   29 ARG cc_start: 0.8514 (ptt-90) cc_final: 0.7591 (ptt-90)
REVERT: Y   30 MET cc_start: 0.9108 (mmp) cc_final: 0.8876 (mmp)
REVERT: 0   11 LYS cc_start: 0.9532 (mmmm) cc_final: 0.9279 (mmmm)
REVERT: 0   14 MET cc_start: 0.9296 (mpp) cc_final: 0.8995 (mpp)
REVERT: 0   19 ASP cc_start: 0.8794 (m-30) cc_final: 0.8486 (m-30)
REVERT: 2   22 MET cc_start: 0.8664 (tpp) cc_final: 0.8363 (mmm)
REVERT: Z   20 LYS cc_start: 0.9411 (tptm) cc_final: 0.9029 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.5597
  time to fit residues: 192.2035
Evaluate side-chains
  166 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 2.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 280 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 165 optimal weight:    9.9990
   chunk 212 optimal weight:    7.9990
   chunk 164 optimal weight:    3.9990
   chunk 245 optimal weight:    2.9990
   chunk 162 optimal weight:    4.9990
   chunk 290 optimal weight:   20.0000
   chunk 181 optimal weight:    7.9990
   chunk 176 optimal weight:    0.8980
   chunk 133 optimal weight:   40.0000
   overall best weight:    3.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
J 128 ASN
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.6395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  48167  Z= 0.173
  Angle     :  0.545   9.340  72350  Z= 0.276
  Chirality :  0.031   0.287   9318
  Planarity :  0.004   0.055   3647
  Dihedral  : 24.295 178.772  24691
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 23.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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: -1.21 (0.20), residues: 1569
  helix:  0.48 (0.23), residues: 482
  sheet: -1.09 (0.28), residues: 283
  loop : -1.50 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  78 
 HIS   0.009   0.001   HIS N  16 
 PHE   0.046   0.001   PHE N  21 
 TYR   0.010   0.001   TYR N 112 
 ARG   0.016   0.001   ARG L   2 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 2.409 
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: D   11 MET cc_start: 0.7759 (ppp) cc_final: 0.7513 (ppp)
REVERT: E    9 GLN cc_start: 0.8721 (mp-120) cc_final: 0.8439 (mp-120)
REVERT: E   19 PHE cc_start: 0.8326 (m-80) cc_final: 0.7948 (m-80)
REVERT: E  100 MET cc_start: 0.9610 (pmm) cc_final: 0.9396 (pmm)
REVERT: E  188 MET cc_start: 0.8798 (ptm) cc_final: 0.8490 (ptm)
REVERT: J   53 TYR cc_start: 0.8947 (m-80) cc_final: 0.7760 (m-80)
REVERT: J   67 ASN cc_start: 0.8728 (t0) cc_final: 0.8231 (t0)
REVERT: J   92 MET cc_start: 0.9653 (ttm) cc_final: 0.9048 (tpp)
REVERT: J  108 MET cc_start: 0.8201 (tpt) cc_final: 0.7901 (mmm)
REVERT: K   79 PHE cc_start: 0.9144 (m-80) cc_final: 0.8895 (m-80)
REVERT: N   13 ASN cc_start: 0.8981 (t0) cc_final: 0.8665 (t0)
REVERT: N   20 MET cc_start: 0.9094 (ttm) cc_final: 0.8754 (tmm)
REVERT: N   21 PHE cc_start: 0.9240 (m-80) cc_final: 0.8729 (m-80)
REVERT: P   12 MET cc_start: 0.9208 (mmt) cc_final: 0.8101 (mmp)
REVERT: Q   21 LYS cc_start: 0.9466 (mmtt) cc_final: 0.9169 (pttt)
REVERT: Q   48 ASP cc_start: 0.8581 (t0) cc_final: 0.7948 (t0)
REVERT: R   70 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7785 (tm-30)
REVERT: R   71 LYS cc_start: 0.9025 (tptp) cc_final: 0.8774 (tptt)
REVERT: R   74 ILE cc_start: 0.9092 (mm) cc_final: 0.8786 (mm)
REVERT: R   83 TYR cc_start: 0.7778 (t80) cc_final: 0.7147 (t80)
REVERT: R   85 LYS cc_start: 0.9436 (tmtt) cc_final: 0.9094 (tptt)
REVERT: R   87 GLN cc_start: 0.8951 (pp30) cc_final: 0.8637 (pm20)
REVERT: S   49 LYS cc_start: 0.9655 (tptt) cc_final: 0.9100 (tptm)
REVERT: S   74 ILE cc_start: 0.9334 (tt) cc_final: 0.8906 (pt)
REVERT: S   82 MET cc_start: 0.7192 (tpp) cc_final: 0.6858 (tpp)
REVERT: U    9 GLU cc_start: 0.8182 (tt0) cc_final: 0.7609 (tt0)
REVERT: Y    7 ARG cc_start: 0.8764 (ptt180) cc_final: 0.8232 (ptt180)
REVERT: Y   29 ARG cc_start: 0.8471 (ptt-90) cc_final: 0.7554 (ptt-90)
REVERT: Y   30 MET cc_start: 0.9064 (mmp) cc_final: 0.8833 (mmm)
REVERT: 0    6 LYS cc_start: 0.8801 (tttt) cc_final: 0.8369 (tttm)
REVERT: 0   11 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9248 (mmmm)
REVERT: 0   14 MET cc_start: 0.9252 (mpp) cc_final: 0.8999 (mpp)
REVERT: 0   19 ASP cc_start: 0.8812 (m-30) cc_final: 0.8496 (m-30)
REVERT: 2   22 MET cc_start: 0.8730 (tpp) cc_final: 0.8494 (mmm)
REVERT: Z   20 LYS cc_start: 0.9398 (tptm) cc_final: 0.9005 (tptt)
REVERT: Z   53 MET cc_start: 0.8596 (mmt) cc_final: 0.8043 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.5781
  time to fit residues: 204.3196
Evaluate side-chains
  165 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 2.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 179 optimal weight:    0.5980
   chunk 115 optimal weight:   10.0000
   chunk 173 optimal weight:   20.0000
   chunk 87 optimal weight:   40.0000
   chunk 57 optimal weight:   20.0000
   chunk 56 optimal weight:   10.0000
   chunk 184 optimal weight:    6.9990
   chunk 197 optimal weight:   50.0000
   chunk 143 optimal weight:   20.0000
   chunk 27 optimal weight:   50.0000
   chunk 228 optimal weight:    0.0980
   overall best weight:    5.5390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   4 ASN
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.6715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  48167  Z= 0.223
  Angle     :  0.586   8.552  72350  Z= 0.297
  Chirality :  0.033   0.299   9318
  Planarity :  0.004   0.063   3647
  Dihedral  : 24.409 178.511  24691
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 28.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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: -1.26 (0.20), residues: 1569
  helix:  0.51 (0.23), residues: 473
  sheet: -1.17 (0.28), residues: 282
  loop : -1.53 (0.21), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP P  30 
 HIS   0.005   0.001   HIS R  89 
 PHE   0.036   0.002   PHE N  21 
 TYR   0.011   0.001   TYR J  16 
 ARG   0.014   0.001   ARG L   2 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 2.507 
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: D   38 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8171 (tppt)
REVERT: E   19 PHE cc_start: 0.8303 (m-80) cc_final: 0.7900 (m-80)
REVERT: E  100 MET cc_start: 0.9621 (pmm) cc_final: 0.9396 (pmm)
REVERT: E  188 MET cc_start: 0.8725 (ptm) cc_final: 0.8269 (ptm)
REVERT: J   53 TYR cc_start: 0.8987 (m-80) cc_final: 0.7856 (m-80)
REVERT: J   67 ASN cc_start: 0.8737 (t0) cc_final: 0.8277 (t0)
REVERT: J   92 MET cc_start: 0.9659 (ttm) cc_final: 0.9097 (tpp)
REVERT: J  108 MET cc_start: 0.8294 (tpt) cc_final: 0.7967 (mmm)
REVERT: J  114 LEU cc_start: 0.9017 (mp) cc_final: 0.8519 (mp)
REVERT: K   79 PHE cc_start: 0.9168 (m-80) cc_final: 0.8942 (m-80)
REVERT: N   10 LEU cc_start: 0.9380 (mp) cc_final: 0.9171 (mp)
REVERT: N   13 ASN cc_start: 0.9107 (t0) cc_final: 0.8688 (t0)
REVERT: N   20 MET cc_start: 0.9097 (ttm) cc_final: 0.8711 (tmm)
REVERT: N   21 PHE cc_start: 0.9282 (m-80) cc_final: 0.8832 (m-80)
REVERT: P   12 MET cc_start: 0.9153 (mmt) cc_final: 0.8019 (mmm)
REVERT: P   58 PHE cc_start: 0.8945 (p90) cc_final: 0.8435 (p90)
REVERT: Q   21 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9176 (pttt)
REVERT: Q   48 ASP cc_start: 0.8649 (t0) cc_final: 0.7970 (t0)
REVERT: R   83 TYR cc_start: 0.7878 (t80) cc_final: 0.7255 (t80)
REVERT: R   85 LYS cc_start: 0.9461 (tmtt) cc_final: 0.9147 (tptp)
REVERT: R   87 GLN cc_start: 0.8678 (pp30) cc_final: 0.7887 (pp30)
REVERT: S   38 TYR cc_start: 0.8514 (m-10) cc_final: 0.8189 (m-10)
REVERT: S   49 LYS cc_start: 0.9647 (tptt) cc_final: 0.9374 (tptm)
REVERT: S   68 ASP cc_start: 0.8158 (p0) cc_final: 0.7776 (p0)
REVERT: S   82 MET cc_start: 0.7204 (tpp) cc_final: 0.6878 (tpp)
REVERT: U    9 GLU cc_start: 0.8233 (tt0) cc_final: 0.7934 (tt0)
REVERT: Y   30 MET cc_start: 0.9076 (mmp) cc_final: 0.8776 (mmp)
REVERT: 0    6 LYS cc_start: 0.8820 (tttt) cc_final: 0.8350 (tttm)
REVERT: 0   11 LYS cc_start: 0.9507 (mmmm) cc_final: 0.9242 (mmmm)
REVERT: 0   14 MET cc_start: 0.9189 (mpp) cc_final: 0.8957 (mpp)
REVERT: 0   19 ASP cc_start: 0.8833 (m-30) cc_final: 0.8510 (m-30)
REVERT: Z   20 LYS cc_start: 0.9414 (tptm) cc_final: 0.9019 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.5867
  time to fit residues: 201.3836
Evaluate side-chains
  161 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 2.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 263 optimal weight:    5.9990
   chunk 277 optimal weight:   20.0000
   chunk 253 optimal weight:    8.9990
   chunk 270 optimal weight:    3.9990
   chunk 162 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 212 optimal weight:    9.9990
   chunk 82 optimal weight:   20.0000
   chunk 244 optimal weight:   10.0000
   chunk 255 optimal weight:    8.9990
   chunk 269 optimal weight:   10.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.7082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  48167  Z= 0.250
  Angle     :  0.614   8.372  72350  Z= 0.311
  Chirality :  0.034   0.314   9318
  Planarity :  0.005   0.050   3647
  Dihedral  : 24.528 178.801  24691
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 30.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  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: -1.52 (0.20), residues: 1569
  helix:  0.24 (0.23), residues: 478
  sheet: -1.53 (0.27), residues: 307
  loop : -1.55 (0.21), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R  92 
 HIS   0.004   0.001   HIS R  66 
 PHE   0.033   0.002   PHE N  21 
 TYR   0.011   0.002   TYR J  16 
 ARG   0.013   0.001   ARG L   2 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 2.455 
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: D   11 MET cc_start: 0.7863 (ppp) cc_final: 0.7570 (ppp)
REVERT: D   38 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8219 (tppt)
REVERT: E   19 PHE cc_start: 0.8303 (m-80) cc_final: 0.7878 (m-80)
REVERT: E  188 MET cc_start: 0.8740 (ptm) cc_final: 0.8442 (ptm)
REVERT: J   53 TYR cc_start: 0.8971 (m-80) cc_final: 0.7835 (m-80)
REVERT: J   67 ASN cc_start: 0.8740 (t0) cc_final: 0.8273 (t0)
REVERT: J   71 ASP cc_start: 0.8409 (m-30) cc_final: 0.7922 (m-30)
REVERT: J   92 MET cc_start: 0.9675 (ttm) cc_final: 0.9438 (ttm)
REVERT: J  108 MET cc_start: 0.8300 (tpt) cc_final: 0.7928 (mmm)
REVERT: J  114 LEU cc_start: 0.9066 (mp) cc_final: 0.8533 (mp)
REVERT: K    1 MET cc_start: 0.5387 (tmm) cc_final: 0.4685 (pmm)
REVERT: K   87 LEU cc_start: 0.6870 (mp) cc_final: 0.6623 (mp)
REVERT: N   13 ASN cc_start: 0.9180 (t0) cc_final: 0.8774 (t0)
REVERT: N   20 MET cc_start: 0.9090 (ttm) cc_final: 0.8686 (tmm)
REVERT: N   21 PHE cc_start: 0.9241 (m-80) cc_final: 0.8727 (m-80)
REVERT: Q   21 LYS cc_start: 0.9484 (mmtt) cc_final: 0.9178 (pttt)
REVERT: Q   48 ASP cc_start: 0.8750 (t0) cc_final: 0.8010 (t0)
REVERT: R   45 GLU cc_start: 0.8920 (mp0) cc_final: 0.8666 (mp0)
REVERT: R   71 LYS cc_start: 0.8986 (tptp) cc_final: 0.8682 (tptt)
REVERT: R   74 ILE cc_start: 0.9196 (mm) cc_final: 0.8855 (mm)
REVERT: R   83 TYR cc_start: 0.7947 (t80) cc_final: 0.7558 (t80)
REVERT: R   85 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9176 (tptp)
REVERT: S   49 LYS cc_start: 0.9683 (tptt) cc_final: 0.9436 (tptm)
REVERT: S   65 ASP cc_start: 0.8467 (t0) cc_final: 0.8138 (t0)
REVERT: S   82 MET cc_start: 0.7301 (tpp) cc_final: 0.7021 (tpp)
REVERT: S  109 ASP cc_start: 0.7966 (m-30) cc_final: 0.7546 (m-30)
REVERT: U    9 GLU cc_start: 0.8194 (tt0) cc_final: 0.7888 (tt0)
REVERT: Y    7 ARG cc_start: 0.8805 (ptt180) cc_final: 0.8455 (ptt90)
REVERT: Y   29 ARG cc_start: 0.8268 (ptt-90) cc_final: 0.7565 (ptt-90)
REVERT: Y   30 MET cc_start: 0.9116 (mmp) cc_final: 0.8825 (mmp)
REVERT: 0    6 LYS cc_start: 0.8862 (tttt) cc_final: 0.8414 (tttm)
REVERT: 0   11 LYS cc_start: 0.9533 (mmmm) cc_final: 0.9253 (mmmm)
REVERT: 0   14 MET cc_start: 0.9240 (mpp) cc_final: 0.8978 (mpp)
REVERT: 0   19 ASP cc_start: 0.8854 (m-30) cc_final: 0.8525 (m-30)
REVERT: 2   14 ARG cc_start: 0.8914 (mmp-170) cc_final: 0.8479 (mmp-170)
REVERT: 2   22 MET cc_start: 0.8839 (tpp) cc_final: 0.8530 (mmm)
REVERT: Z   20 LYS cc_start: 0.9418 (tptm) cc_final: 0.9027 (tptt)
REVERT: Z   53 MET cc_start: 0.8628 (mmt) cc_final: 0.8229 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.5720
  time to fit residues: 192.1432
Evaluate side-chains
  160 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 2.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 177 optimal weight:    5.9990
   chunk 285 optimal weight:    5.9990
   chunk 174 optimal weight:    5.9990
   chunk 135 optimal weight:   20.0000
   chunk 198 optimal weight:    6.9990
   chunk 299 optimal weight:    0.8980
   chunk 275 optimal weight:    7.9990
   chunk 238 optimal weight:   10.0000
   chunk 24 optimal weight:   30.0000
   chunk 184 optimal weight:   30.0000
   chunk 146 optimal weight:   20.0000
   overall best weight:    5.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.7123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  48167  Z= 0.210
  Angle     :  0.577   8.764  72350  Z= 0.292
  Chirality :  0.032   0.313   9318
  Planarity :  0.004   0.053   3647
  Dihedral  : 24.468 178.412  24691
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 27.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.20), residues: 1569
  helix:  0.31 (0.23), residues: 476
  sheet: -1.56 (0.28), residues: 279
  loop : -1.56 (0.20), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP P  30 
 HIS   0.004   0.001   HIS R  12 
 PHE   0.030   0.002   PHE N  21 
 TYR   0.009   0.001   TYR N 112 
 ARG   0.011   0.001   ARG L   2 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.962 
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: D   11 MET cc_start: 0.8195 (ppp) cc_final: 0.7853 (ppp)
REVERT: D   38 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8484 (mmtt)
REVERT: E   19 PHE cc_start: 0.8229 (m-80) cc_final: 0.7827 (m-80)
REVERT: E  100 MET cc_start: 0.9623 (pmm) cc_final: 0.9422 (pmm)
REVERT: E  188 MET cc_start: 0.8716 (ptm) cc_final: 0.8213 (ptm)
REVERT: J   53 TYR cc_start: 0.8973 (m-80) cc_final: 0.7890 (m-80)
REVERT: J   67 ASN cc_start: 0.8766 (t0) cc_final: 0.8282 (t0)
REVERT: J   71 ASP cc_start: 0.8440 (m-30) cc_final: 0.7967 (m-30)
REVERT: J  108 MET cc_start: 0.8284 (tpt) cc_final: 0.7889 (mmm)
REVERT: J  114 LEU cc_start: 0.9078 (mp) cc_final: 0.8580 (mp)
REVERT: K    1 MET cc_start: 0.5128 (tmm) cc_final: 0.4783 (pmm)
REVERT: K   79 PHE cc_start: 0.9309 (m-80) cc_final: 0.8960 (m-80)
REVERT: K   87 LEU cc_start: 0.7183 (mp) cc_final: 0.6936 (mp)
REVERT: N   10 LEU cc_start: 0.9442 (mp) cc_final: 0.9232 (mp)
REVERT: N   13 ASN cc_start: 0.9059 (t0) cc_final: 0.8674 (t0)
REVERT: N   20 MET cc_start: 0.9097 (ttm) cc_final: 0.8671 (tmm)
REVERT: N   21 PHE cc_start: 0.9249 (m-80) cc_final: 0.8782 (m-80)
REVERT: Q   21 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9174 (pttt)
REVERT: Q   48 ASP cc_start: 0.8772 (t0) cc_final: 0.7943 (t0)
REVERT: R   45 GLU cc_start: 0.8864 (mp0) cc_final: 0.8608 (mp0)
REVERT: R   74 ILE cc_start: 0.9073 (mm) cc_final: 0.8833 (mm)
REVERT: S    1 MET cc_start: 0.5621 (ptt) cc_final: 0.4447 (pmm)
REVERT: S   38 TYR cc_start: 0.8487 (m-10) cc_final: 0.8172 (m-10)
REVERT: S   49 LYS cc_start: 0.9660 (tptt) cc_final: 0.9385 (tptm)
REVERT: S   65 ASP cc_start: 0.8473 (t0) cc_final: 0.8165 (t0)
REVERT: S   82 MET cc_start: 0.7338 (tpp) cc_final: 0.7120 (mpp)
REVERT: S  109 ASP cc_start: 0.8093 (m-30) cc_final: 0.7623 (m-30)
REVERT: U    9 GLU cc_start: 0.8218 (tt0) cc_final: 0.7921 (tt0)
REVERT: Y    7 ARG cc_start: 0.8789 (ptt180) cc_final: 0.8412 (ptt90)
REVERT: Y   29 ARG cc_start: 0.8260 (ptt-90) cc_final: 0.7550 (ptt-90)
REVERT: Y   30 MET cc_start: 0.9097 (mmp) cc_final: 0.8793 (mmp)
REVERT: 0    6 LYS cc_start: 0.8866 (tttt) cc_final: 0.8447 (tttm)
REVERT: 0   11 LYS cc_start: 0.9521 (mmmm) cc_final: 0.9249 (mmmm)
REVERT: 0   14 MET cc_start: 0.9247 (mpp) cc_final: 0.8992 (mpp)
REVERT: 0   19 ASP cc_start: 0.8918 (m-30) cc_final: 0.8614 (m-30)
REVERT: 2   14 ARG cc_start: 0.8976 (mmp-170) cc_final: 0.8702 (mmp-170)
REVERT: 2   22 MET cc_start: 0.8825 (tpp) cc_final: 0.8514 (mmm)
REVERT: Z   20 LYS cc_start: 0.9406 (tptm) cc_final: 0.8888 (tptt)
REVERT: Z   24 LEU cc_start: 0.9663 (pp) cc_final: 0.9451 (pp)
REVERT: Z   53 MET cc_start: 0.8580 (mmt) cc_final: 0.8202 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.5768
  time to fit residues: 196.5141
Evaluate side-chains
  160 residues out of total 1308 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 2.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 189 optimal weight:    7.9990
   chunk 254 optimal weight:    5.9990
   chunk 73 optimal weight:   20.0000
   chunk 220 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 239 optimal weight:   50.0000
   chunk 100 optimal weight:   20.0000
   chunk 245 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   overall best weight:    8.7994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  57 ASN
** U  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
2  13 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.042606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.030260 restraints weight = 515969.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.031178 restraints weight = 233887.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.031695 restraints weight = 152595.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.7908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  48167  Z= 0.331
  Angle     :  0.723  10.992  72350  Z= 0.364
  Chirality :  0.039   0.336   9318
  Planarity :  0.005   0.050   3647
  Dihedral  : 24.912 179.001  24691
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 39.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -1.84 (0.20), residues: 1569
  helix: -0.01 (0.23), residues: 470
  sheet: -1.75 (0.27), residues: 296
  loop : -1.74 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP R  92 
 HIS   0.006   0.001   HIS R  66 
 PHE   0.035   0.002   PHE N  21 
 TYR   0.012   0.002   TYR Q  46 
 ARG   0.010   0.001   ARG L   2 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5850.74 seconds
wall clock time: 110 minutes 49.83 seconds (6649.83 seconds total)