Starting phenix.real_space_refine
on Tue Aug 26 23:47:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c96_16503/08_2025/8c96_16503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c96_16503/08_2025/8c96_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/cci-nas-00/data/ceres_data/8c96_16503/08_2025/8c96_16503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2025/8c96_16503.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2025/8c96_16503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2025/8c96_16503.cif"
  }
  resolution = 4.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
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
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 10.72, per 1000 atoms: 0.24
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.88
  Conformation dependent library (CDL) restraints added in 945.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 8.20
  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: 23.78

  Time building geometry restraints manager: 5.27 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:
        0.00 -     1.16: 71332
        1.16 -     2.31: 870
        2.31 -     3.47: 113
        3.47 -     4.62: 31
        4.62 -     5.78: 4
  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 3.040
  nonbonded pdb=" O2'   A A2632 "
            pdb=" O2'   G A2811 "
     model   vdw
     1.941 3.040
  nonbonded pdb=" O2'   G A 214 "
            pdb=" O4'   G A 215 "
     model   vdw
     1.949 3.040
  nonbonded pdb=" OP2   G A 117 "
            pdb=" O2'   A A 119 "
     model   vdw
     1.957 3.040
  nonbonded pdb=" O2'   G A 261 "
            pdb=" O2'   C A 610 "
     model   vdw
     1.972 3.040
  ... (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
Time spend for trying shortcut: 0.00
========== 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:             2.500
  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:          0.660
  Check model and map are aligned:         0.120
  Set scattering table:                    0.120
  Process input model:                     60.410
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   65.590
-------------------------------------------------------------------------------
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= 0.080
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG 0  12 
 TYR   0.008   0.001   TYR N 112 
 PHE   0.006   0.001   PHE Z  52 
 TRP   0.004   0.001   TRP R  92 
 HIS   0.002   0.000   HIS S 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00147 (48167)
  covalent geometry    : angle       0.36405 (72350)
  hydrogen bonds       : bond        0.09920 ( 1693)
  hydrogen bonds       : angle       4.12062 ( 3296)

*********************** 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 to be fit.
    rotamer outliers: 1
    poor density    : 311
  time to evaluate  : 0.848 
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: 0.3079
  time to fit residues: 153.0143
Evaluate side-chains
  192 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 197 optimal weight:   20.0000
   chunk 215 optimal weight:   50.0000
   chunk 20 optimal weight:   20.0000
   chunk 132 optimal weight:   40.0000
   chunk 261 optimal weight:    7.9990
   chunk 248 optimal weight:    8.9990
   chunk 207 optimal weight:    0.9980
   chunk 155 optimal weight:    5.9990
   chunk 244 optimal weight:    0.9980
   chunk 183 optimal weight:    0.6980
   chunk 298 optimal weight:    8.9990
   overall best weight:    3.3384

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

Flipped N/Q/H residues before XYZ refinement:
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 HIS
D  94 GLN
J  47 HIS
J 132 HIS
P  65 ASN
P  76 HIS
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  82 HIS
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.052601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.039462 restraints weight = 489536.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.040616 restraints weight = 225467.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.041251 restraints weight = 146276.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.041639 restraints weight = 115742.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.041804 restraints weight = 101542.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  48167  Z= 0.143
  Angle     :  0.518   9.911  72350  Z= 0.260
  Chirality :  0.029   0.209   9318
  Planarity :  0.004   0.071   3647
  Dihedral  : 23.478 175.406  24691
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.21), residues: 1569
  helix:  1.23 (0.24), residues: 482
  sheet:  0.31 (0.32), residues: 255
  loop : -0.91 (0.21), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  59 
 TYR   0.011   0.001   TYR N 112 
 PHE   0.021   0.001   PHE N  21 
 TRP   0.027   0.004   TRP E  78 
 HIS   0.003   0.001   HIS D  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (48167)
  covalent geometry    : angle       0.51756 (72350)
  hydrogen bonds       : bond        0.06637 ( 1693)
  hydrogen bonds       : angle       3.58035 ( 3296)

*********************** 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
  265 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   41 GLN cc_start: 0.8961 (tp40) cc_final: 0.8434 (tp40)
REVERT: E  115 GLN cc_start: 0.9215 (tp40) cc_final: 0.8863 (tp40)
REVERT: E  188 MET cc_start: 0.8948 (ptm) cc_final: 0.8748 (ptm)
REVERT: J   53 TYR cc_start: 0.8473 (m-10) cc_final: 0.7965 (m-80)
REVERT: J   67 ASN cc_start: 0.7427 (t0) cc_final: 0.6906 (t0)
REVERT: K    3 GLN cc_start: 0.6109 (pm20) cc_final: 0.5527 (pm20)
REVERT: K    7 MET cc_start: 0.7473 (tpt) cc_final: 0.7164 (tmm)
REVERT: K   58 LEU cc_start: 0.6975 (tp) cc_final: 0.6534 (tp)
REVERT: K   79 PHE cc_start: 0.9279 (m-80) cc_final: 0.8728 (m-80)
REVERT: N   13 ASN cc_start: 0.9043 (m-40) cc_final: 0.8706 (m-40)
REVERT: N   20 MET cc_start: 0.8983 (ttm) cc_final: 0.8407 (tmm)
REVERT: N   21 PHE cc_start: 0.8909 (m-80) cc_final: 0.8671 (m-80)
REVERT: N   43 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8895 (mm-30)
REVERT: P   12 MET cc_start: 0.8760 (mmt) cc_final: 0.8274 (mmm)
REVERT: P   37 LYS cc_start: 0.6655 (tppt) cc_final: 0.6441 (tppt)
REVERT: P   73 PHE cc_start: 0.7809 (m-80) cc_final: 0.7341 (m-80)
REVERT: Q   36 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8506 (tm-30)
REVERT: Q   48 ASP cc_start: 0.8075 (t0) cc_final: 0.7360 (t0)
REVERT: R   27 ILE cc_start: 0.8287 (mm) cc_final: 0.7835 (mm)
REVERT: R   31 GLU cc_start: 0.9376 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: R   85 LYS cc_start: 0.9285 (tttp) cc_final: 0.9068 (tttp)
REVERT: R   86 GLN cc_start: 0.7813 (pp30) cc_final: 0.7543 (pp30)
REVERT: R   87 GLN cc_start: 0.8294 (pp30) cc_final: 0.7487 (pp30)
REVERT: S   49 LYS cc_start: 0.9566 (tptt) cc_final: 0.8929 (tptt)
REVERT: S   68 ASP cc_start: 0.8032 (p0) cc_final: 0.7656 (p0)
REVERT: S   74 ILE cc_start: 0.9113 (tt) cc_final: 0.8597 (pt)
REVERT: S   99 ARG cc_start: 0.8262 (mpt180) cc_final: 0.8008 (mpt180)
REVERT: S  103 ILE cc_start: 0.9550 (pt) cc_final: 0.9211 (mp)
REVERT: Y    1 MET cc_start: 0.7998 (ppp) cc_final: 0.7195 (ppp)
REVERT: Y   29 ARG cc_start: 0.8239 (ptt-90) cc_final: 0.7658 (ptt-90)
REVERT: Y   30 MET cc_start: 0.8868 (mmp) cc_final: 0.8668 (mmm)
REVERT: Y   45 GLN cc_start: 0.9410 (tt0) cc_final: 0.9188 (tm-30)
REVERT: 0   36 LYS cc_start: 0.9298 (mppt) cc_final: 0.9093 (mmtp)
REVERT: Z   20 LYS cc_start: 0.9327 (tptm) cc_final: 0.8898 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.2848
  time to fit residues: 123.5384
Evaluate side-chains
  189 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 157 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 158 optimal weight:   10.0000
   chunk 204 optimal weight:   50.0000
   chunk 256 optimal weight:    0.8980
   chunk 131 optimal weight:   40.0000
   chunk 106 optimal weight:   40.0000
   chunk 66 optimal weight:   20.0000
   chunk 172 optimal weight:    0.0980
   chunk 238 optimal weight:    7.9990
   overall best weight:    5.7988

-------------------------------------------------------------------------------
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
D 164 GLN
J 135 GLN
N 107 ASN
P   9 GLN
P  40 GLN
P  65 ASN
R  18 GLN
U  68 ASN
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.047498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.034553 restraints weight = 487643.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.035583 restraints weight = 224360.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.036175 restraints weight = 145502.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.036498 restraints weight = 114892.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.036682 restraints weight = 101767.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  48167  Z= 0.221
  Angle     :  0.618  10.954  72350  Z= 0.312
  Chirality :  0.033   0.273   9318
  Planarity :  0.005   0.083   3647
  Dihedral  : 24.019 176.418  24691
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 19.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.96 %
    Favored  : 93.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.20), residues: 1569
  helix:  0.65 (0.23), residues: 493
  sheet: -0.62 (0.30), residues: 256
  loop : -1.09 (0.20), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG R  21 
 TYR   0.013   0.002   TYR J  53 
 PHE   0.020   0.002   PHE E  19 
 TRP   0.026   0.004   TRP P  30 
 HIS   0.010   0.002   HIS N   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (48167)
  covalent geometry    : angle       0.61763 (72350)
  hydrogen bonds       : bond        0.08850 ( 1693)
  hydrogen bonds       : angle       3.87636 ( 3296)

*********************** 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
  239 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 237
  time to evaluate  : 1.093 
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  188 MET cc_start: 0.8830 (ptm) cc_final: 0.8564 (ptm)
REVERT: J   53 TYR cc_start: 0.8926 (m-80) cc_final: 0.8188 (m-80)
REVERT: J   67 ASN cc_start: 0.8093 (t0) cc_final: 0.7545 (t0)
REVERT: J   92 MET cc_start: 0.9585 (ttm) cc_final: 0.9208 (tpp)
REVERT: K    1 MET cc_start: 0.6220 (tmm) cc_final: 0.5958 (tpp)
REVERT: K    7 MET cc_start: 0.7939 (tpt) cc_final: 0.7628 (tmm)
REVERT: K   58 LEU cc_start: 0.6949 (tp) cc_final: 0.6522 (tp)
REVERT: K   65 THR cc_start: 0.9023 (p) cc_final: 0.8814 (p)
REVERT: K   79 PHE cc_start: 0.9255 (m-80) cc_final: 0.8742 (m-10)
REVERT: N   13 ASN cc_start: 0.9104 (m-40) cc_final: 0.8851 (m-40)
REVERT: N   20 MET cc_start: 0.8988 (ttm) cc_final: 0.8367 (tmm)
REVERT: N   21 PHE cc_start: 0.9050 (m-80) cc_final: 0.8690 (m-80)
REVERT: N   28 LEU cc_start: 0.9269 (tt) cc_final: 0.9068 (tp)
REVERT: P    9 GLN cc_start: 0.8599 (mp10) cc_final: 0.8390 (mm-40)
REVERT: P   58 PHE cc_start: 0.9007 (p90) cc_final: 0.8781 (p90)
REVERT: Q   48 ASP cc_start: 0.8378 (t0) cc_final: 0.7733 (t0)
REVERT: R   70 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: R   85 LYS cc_start: 0.9358 (tttp) cc_final: 0.9128 (tttp)
REVERT: R   86 GLN cc_start: 0.7961 (pp30) cc_final: 0.7732 (pp30)
REVERT: R   87 GLN cc_start: 0.8509 (pp30) cc_final: 0.7679 (pp30)
REVERT: S   49 LYS cc_start: 0.9547 (tptt) cc_final: 0.8886 (tptt)
REVERT: S   68 ASP cc_start: 0.8061 (p0) cc_final: 0.7600 (p0)
REVERT: S   74 ILE cc_start: 0.9246 (tt) cc_final: 0.8845 (pt)
REVERT: S  103 ILE cc_start: 0.9610 (pt) cc_final: 0.9362 (mp)
REVERT: U   88 ASP cc_start: 0.9145 (m-30) cc_final: 0.8710 (p0)
REVERT: Y    1 MET cc_start: 0.8251 (ppp) cc_final: 0.7461 (ppp)
REVERT: Y   18 LEU cc_start: 0.8797 (pp) cc_final: 0.8555 (tp)
REVERT: Y   29 ARG cc_start: 0.8191 (ptt-90) cc_final: 0.7532 (ptt-90)
REVERT: Y   30 MET cc_start: 0.8901 (mmp) cc_final: 0.8590 (mmm)
REVERT: 0    6 LYS cc_start: 0.9026 (tttt) cc_final: 0.8179 (tmtt)
REVERT: 2   14 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.7235 (mmp80)
REVERT: Z   20 LYS cc_start: 0.9363 (tptm) cc_final: 0.8945 (tptp)
  outliers start: 2
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2794
  time to fit residues: 110.5978
Evaluate side-chains
  180 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 140 optimal weight:   10.0000
   chunk 177 optimal weight:    0.0970
   chunk 16 optimal weight:   30.0000
   chunk 162 optimal weight:    5.9990
   chunk 203 optimal weight:   20.0000
   chunk 242 optimal weight:    9.9990
   chunk 212 optimal weight:    7.9990
   chunk 40 optimal weight:   40.0000
   chunk 293 optimal weight:    5.9990
   chunk 200 optimal weight:   40.0000
   chunk 281 optimal weight:   20.0000
   overall best weight:    6.0186

-------------------------------------------------------------------------------
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  94 GLN
K   3 GLN
N 107 ASN
P  40 GLN
P  65 ASN
** Q  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  11 GLN
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  66 HIS
** Y  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.046501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.033663 restraints weight = 489250.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.034667 restraints weight = 224746.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.035246 restraints weight = 145188.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.035583 restraints weight = 114859.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.035718 restraints weight = 101037.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  48167  Z= 0.211
  Angle     :  0.590   9.035  72350  Z= 0.299
  Chirality :  0.033   0.207   9318
  Planarity :  0.005   0.048   3647
  Dihedral  : 24.142 179.549  24691
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.82 %
    Favored  : 95.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.20), residues: 1569
  helix:  0.61 (0.23), residues: 489
  sheet: -0.72 (0.29), residues: 281
  loop : -1.28 (0.20), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Q  50 
 TYR   0.014   0.002   TYR R  83 
 PHE   0.018   0.002   PHE N  21 
 TRP   0.014   0.002   TRP P  30 
 HIS   0.008   0.001   HIS J  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (48167)
  covalent geometry    : angle       0.58970 (72350)
  hydrogen bonds       : bond        0.08166 ( 1693)
  hydrogen bonds       : angle       3.73948 ( 3296)

*********************** 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
  216 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 214
  time to evaluate  : 0.907 
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: D   11 MET cc_start: 0.8255 (ppp) cc_final: 0.7955 (ppp)
REVERT: E  188 MET cc_start: 0.8814 (ptm) cc_final: 0.8472 (ptm)
REVERT: J   53 TYR cc_start: 0.9151 (m-80) cc_final: 0.8262 (m-80)
REVERT: J   67 ASN cc_start: 0.8556 (t0) cc_final: 0.7970 (t0)
REVERT: J   92 MET cc_start: 0.9587 (ttm) cc_final: 0.9173 (tpp)
REVERT: K    7 MET cc_start: 0.7822 (tpt) cc_final: 0.7608 (tmm)
REVERT: K   58 LEU cc_start: 0.6823 (tp) cc_final: 0.6480 (tp)
REVERT: K   79 PHE cc_start: 0.9212 (m-80) cc_final: 0.8766 (m-80)
REVERT: N   20 MET cc_start: 0.9036 (ttm) cc_final: 0.8482 (tmm)
REVERT: N   21 PHE cc_start: 0.9157 (m-80) cc_final: 0.8946 (m-80)
REVERT: N  102 PHE cc_start: 0.8761 (m-10) cc_final: 0.8484 (m-10)
REVERT: P    9 GLN cc_start: 0.8647 (mp10) cc_final: 0.8349 (mm-40)
REVERT: P   58 PHE cc_start: 0.8905 (p90) cc_final: 0.8644 (p90)
REVERT: Q   48 ASP cc_start: 0.8398 (t0) cc_final: 0.7765 (t0)
REVERT: R   70 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: R   71 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8827 (tptm)
REVERT: R   86 GLN cc_start: 0.8025 (pp30) cc_final: 0.7780 (pp30)
REVERT: S   49 LYS cc_start: 0.9489 (tptt) cc_final: 0.8692 (tptm)
REVERT: S   68 ASP cc_start: 0.7901 (p0) cc_final: 0.7499 (p0)
REVERT: S   78 GLU cc_start: 0.8277 (mp0) cc_final: 0.8029 (mp0)
REVERT: S   99 ARG cc_start: 0.8572 (mpt180) cc_final: 0.8003 (mpt180)
REVERT: S  103 ILE cc_start: 0.9628 (pt) cc_final: 0.9394 (mp)
REVERT: Y    1 MET cc_start: 0.8561 (ppp) cc_final: 0.8199 (ppp)
REVERT: Y   13 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8492 (mp0)
REVERT: Y   23 ARG cc_start: 0.8709 (pmt-80) cc_final: 0.8503 (pmt-80)
REVERT: Y   30 MET cc_start: 0.9008 (mmp) cc_final: 0.8671 (mmp)
REVERT: 0    6 LYS cc_start: 0.9083 (tttt) cc_final: 0.8240 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9114 (mmmm)
REVERT: 2   14 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.8043 (mmm160)
REVERT: 2   22 MET cc_start: 0.8778 (tpp) cc_final: 0.8561 (mmm)
REVERT: Z   20 LYS cc_start: 0.9371 (tptm) cc_final: 0.8975 (tptp)
REVERT: Z   51 SER cc_start: 0.9163 (p) cc_final: 0.8778 (m)
  outliers start: 2
  outliers final: 2
  residues processed: 216
  average time/residue: 0.2676
  time to fit residues: 97.0917
Evaluate side-chains
  171 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 147 optimal weight:    6.9990
   chunk 215 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 189 optimal weight:    6.9990
   chunk 252 optimal weight:    9.9990
   chunk 264 optimal weight:    0.9980
   chunk 277 optimal weight:    0.0570
   chunk 3 optimal weight:   10.0000
   chunk 285 optimal weight:   20.0000
   chunk 183 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   overall best weight:    5.0104

-------------------------------------------------------------------------------
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  94 GLN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
K  89 ASN
P  65 ASN
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.047785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.035534 restraints weight = 520467.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.036553 restraints weight = 230143.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.037142 restraints weight = 147096.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.037501 restraints weight = 116141.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.037671 restraints weight = 102270.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.5163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  48167  Z= 0.185
  Angle     :  0.565   9.224  72350  Z= 0.285
  Chirality :  0.032   0.206   9318
  Planarity :  0.004   0.046   3647
  Dihedral  : 24.131 178.549  24691
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 18.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.20), residues: 1569
  helix:  0.66 (0.23), residues: 488
  sheet: -0.62 (0.28), residues: 281
  loop : -1.30 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG Z  15 
 TYR   0.009   0.002   TYR N 112 
 PHE   0.017   0.002   PHE N  21 
 TRP   0.012   0.002   TRP P  30 
 HIS   0.005   0.001   HIS P  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (48167)
  covalent geometry    : angle       0.56511 (72350)
  hydrogen bonds       : bond        0.07671 ( 1693)
  hydrogen bonds       : angle       3.68832 ( 3296)

*********************** 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
  232 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 1.094 
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: E  188 MET cc_start: 0.8823 (ptm) cc_final: 0.8425 (ptm)
REVERT: J   53 TYR cc_start: 0.8975 (m-80) cc_final: 0.8259 (m-80)
REVERT: J   67 ASN cc_start: 0.8716 (t0) cc_final: 0.8151 (t0)
REVERT: J   92 MET cc_start: 0.9599 (ttm) cc_final: 0.9182 (tpp)
REVERT: J   93 ILE cc_start: 0.9261 (pt) cc_final: 0.9035 (pt)
REVERT: J  114 LEU cc_start: 0.8870 (mp) cc_final: 0.8364 (mp)
REVERT: K    1 MET cc_start: 0.6371 (tmm) cc_final: 0.4513 (ptt)
REVERT: K    7 MET cc_start: 0.8167 (tpt) cc_final: 0.7848 (tmm)
REVERT: K   58 LEU cc_start: 0.6850 (tp) cc_final: 0.6645 (tp)
REVERT: K   79 PHE cc_start: 0.9253 (m-80) cc_final: 0.8932 (m-80)
REVERT: N   13 ASN cc_start: 0.8730 (t0) cc_final: 0.8468 (t0)
REVERT: N   20 MET cc_start: 0.9083 (ttm) cc_final: 0.8611 (tmm)
REVERT: N   21 PHE cc_start: 0.9147 (m-80) cc_final: 0.8910 (m-80)
REVERT: P   12 MET cc_start: 0.9189 (mmp) cc_final: 0.7922 (mmm)
REVERT: P   58 PHE cc_start: 0.8881 (p90) cc_final: 0.8550 (p90)
REVERT: Q   48 ASP cc_start: 0.8501 (t0) cc_final: 0.8064 (t0)
REVERT: Q   55 GLN cc_start: 0.8923 (mp10) cc_final: 0.8706 (mp10)
REVERT: R   70 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7567 (tm-30)
REVERT: R   71 LYS cc_start: 0.8965 (tmtt) cc_final: 0.8731 (tptm)
REVERT: R   87 GLN cc_start: 0.8498 (pp30) cc_final: 0.8108 (pp30)
REVERT: S   49 LYS cc_start: 0.9524 (tptt) cc_final: 0.9149 (tptm)
REVERT: S   78 GLU cc_start: 0.8234 (mp0) cc_final: 0.7988 (mp0)
REVERT: S   99 ARG cc_start: 0.8368 (mpp-170) cc_final: 0.7869 (mpt180)
REVERT: S  103 ILE cc_start: 0.9595 (pt) cc_final: 0.9376 (mp)
REVERT: U    9 GLU cc_start: 0.8040 (tt0) cc_final: 0.7771 (tt0)
REVERT: U   88 ASP cc_start: 0.9123 (m-30) cc_final: 0.8569 (p0)
REVERT: Y    1 MET cc_start: 0.8330 (ppp) cc_final: 0.7932 (ppp)
REVERT: Y    7 ARG cc_start: 0.8548 (ptt180) cc_final: 0.7932 (ptt180)
REVERT: Y    9 LYS cc_start: 0.8793 (ptmt) cc_final: 0.8565 (ptmm)
REVERT: Y   13 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8281 (mp0)
REVERT: Y   30 MET cc_start: 0.9097 (mmp) cc_final: 0.8753 (mmp)
REVERT: 0    6 LYS cc_start: 0.9057 (tttt) cc_final: 0.8182 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9448 (mmmm) cc_final: 0.9098 (mmmm)
REVERT: 0   14 MET cc_start: 0.9205 (mpp) cc_final: 0.8873 (mpp)
REVERT: 2   14 ARG cc_start: 0.8760 (mmt-90) cc_final: 0.8036 (mmp80)
REVERT: Z   20 LYS cc_start: 0.9368 (tptm) cc_final: 0.8967 (tptp)
REVERT: Z   46 MET cc_start: 0.8633 (mmp) cc_final: 0.8130 (mmp)
REVERT: Z   51 SER cc_start: 0.9166 (p) cc_final: 0.8879 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2817
  time to fit residues: 107.6178
Evaluate side-chains
  171 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 156 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 226 optimal weight:    7.9990
   chunk 118 optimal weight:   20.0000
   chunk 285 optimal weight:    0.0570
   chunk 75 optimal weight:   40.0000
   chunk 255 optimal weight:    9.9990
   chunk 76 optimal weight:   20.0000
   chunk 145 optimal weight:   20.0000
   chunk 168 optimal weight:   20.0000
   chunk 240 optimal weight:    9.9990
   overall best weight:    9.6108

-------------------------------------------------------------------------------
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**
E   9 GLN
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 HIS
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.043009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.030474 restraints weight = 511909.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.031386 restraints weight = 231700.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.031922 restraints weight = 150116.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.032216 restraints weight = 119291.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.032347 restraints weight = 105913.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.6815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.100  48167  Z= 0.330
  Angle     :  0.809  12.299  72350  Z= 0.404
  Chirality :  0.041   0.267   9318
  Planarity :  0.007   0.159   3647
  Dihedral  : 24.854 178.598  24691
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 33.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.06 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.20), residues: 1569
  helix: -0.11 (0.23), residues: 479
  sheet: -1.39 (0.28), residues: 277
  loop : -1.53 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG Q  50 
 TYR   0.015   0.003   TYR N 112 
 PHE   0.026   0.003   PHE N  21 
 TRP   0.033   0.003   TRP P  30 
 HIS   0.007   0.002   HIS R  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 (48167)
  covalent geometry    : angle       0.80900 (72350)
  hydrogen bonds       : bond        0.13091 ( 1693)
  hydrogen bonds       : angle       4.28842 ( 3296)

*********************** 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 to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   53 TYR cc_start: 0.9066 (m-80) cc_final: 0.8180 (m-80)
REVERT: J   67 ASN cc_start: 0.8679 (t0) cc_final: 0.8169 (t0)
REVERT: J   92 MET cc_start: 0.9665 (ttm) cc_final: 0.9169 (tpt)
REVERT: J  108 MET cc_start: 0.8192 (tpt) cc_final: 0.7948 (mmm)
REVERT: J  114 LEU cc_start: 0.8988 (mp) cc_final: 0.8478 (mp)
REVERT: K   65 THR cc_start: 0.9025 (p) cc_final: 0.8820 (p)
REVERT: K   79 PHE cc_start: 0.9266 (m-80) cc_final: 0.8832 (m-10)
REVERT: K  110 GLU cc_start: 0.6029 (mp0) cc_final: 0.5802 (mp0)
REVERT: L   81 ASP cc_start: 0.8337 (t70) cc_final: 0.7166 (m-30)
REVERT: N   13 ASN cc_start: 0.8775 (t0) cc_final: 0.8446 (t0)
REVERT: N   20 MET cc_start: 0.9099 (ttm) cc_final: 0.8651 (tmm)
REVERT: N   21 PHE cc_start: 0.9160 (m-10) cc_final: 0.8765 (m-80)
REVERT: N   79 LEU cc_start: 0.9634 (mt) cc_final: 0.9367 (mt)
REVERT: N  110 MET cc_start: 0.8186 (mpp) cc_final: 0.7814 (mpp)
REVERT: P   12 MET cc_start: 0.9285 (mmp) cc_final: 0.7797 (mmp)
REVERT: P   58 PHE cc_start: 0.8907 (p90) cc_final: 0.8454 (p90)
REVERT: P   84 SER cc_start: 0.7441 (p) cc_final: 0.7119 (p)
REVERT: Q   48 ASP cc_start: 0.8726 (t0) cc_final: 0.8267 (t0)
REVERT: R   70 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7862 (tm-30)
REVERT: S   99 ARG cc_start: 0.8634 (mpp-170) cc_final: 0.7694 (mpt180)
REVERT: S  103 ILE cc_start: 0.9683 (pt) cc_final: 0.9432 (mp)
REVERT: U    9 GLU cc_start: 0.8148 (tt0) cc_final: 0.7861 (tt0)
REVERT: Y    7 ARG cc_start: 0.8696 (ptt180) cc_final: 0.8473 (ptt90)
REVERT: Y   30 MET cc_start: 0.9092 (mmp) cc_final: 0.8792 (mmp)
REVERT: 0    6 LYS cc_start: 0.9004 (tttt) cc_final: 0.8260 (tmtt)
REVERT: 2   14 ARG cc_start: 0.8882 (mmt-90) cc_final: 0.8204 (mmp80)
REVERT: Z   20 LYS cc_start: 0.9425 (tptm) cc_final: 0.8981 (tptt)
REVERT: Z   24 LEU cc_start: 0.9606 (pp) cc_final: 0.9359 (pp)
  outliers start: 1
  outliers final: 1
  residues processed: 208
  average time/residue: 0.2742
  time to fit residues: 95.0099
Evaluate side-chains
  167 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 189 optimal weight:    9.9990
   chunk 286 optimal weight:    5.9990
   chunk 37 optimal weight:   30.0000
   chunk 102 optimal weight:   20.0000
   chunk 296 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 150 optimal weight:    9.9990
   chunk 152 optimal weight:    6.9990
   chunk 197 optimal weight:   30.0000
   chunk 7 optimal weight:   20.0000
   overall best weight:    8.1990

-------------------------------------------------------------------------------
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  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  58 ASN
J 128 ASN
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  80 ASN
R  12 HIS
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.043414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.030875 restraints weight = 497168.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.031790 restraints weight = 226061.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.032309 restraints weight = 147144.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.032609 restraints weight = 117053.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.032736 restraints weight = 103602.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.6888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  48167  Z= 0.274
  Angle     :  0.690   9.771  72350  Z= 0.348
  Chirality :  0.037   0.222   9318
  Planarity :  0.005   0.066   3647
  Dihedral  : 24.692 178.050  24691
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 27.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.20), residues: 1569
  helix: -0.00 (0.23), residues: 485
  sheet: -1.62 (0.29), residues: 267
  loop : -1.55 (0.21), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Q  50 
 TYR   0.012   0.002   TYR R  83 
 PHE   0.019   0.002   PHE N  21 
 TRP   0.024   0.003   TRP P  30 
 HIS   0.010   0.002   HIS U  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (48167)
  covalent geometry    : angle       0.68997 (72350)
  hydrogen bonds       : bond        0.10158 ( 1693)
  hydrogen bonds       : angle       4.07747 ( 3296)

*********************** 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
  207 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.893 
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: 0.8243 (ppp) cc_final: 0.7917 (ppp)
REVERT: J   53 TYR cc_start: 0.9088 (m-80) cc_final: 0.8159 (m-80)
REVERT: J   67 ASN cc_start: 0.8735 (t0) cc_final: 0.8257 (t0)
REVERT: J   92 MET cc_start: 0.9676 (ttm) cc_final: 0.9105 (tpp)
REVERT: J  108 MET cc_start: 0.8300 (tpt) cc_final: 0.8005 (mmm)
REVERT: K   65 THR cc_start: 0.9041 (p) cc_final: 0.8832 (p)
REVERT: K   79 PHE cc_start: 0.9294 (m-80) cc_final: 0.8882 (m-10)
REVERT: L   81 ASP cc_start: 0.8072 (t70) cc_final: 0.6838 (m-30)
REVERT: N   10 LEU cc_start: 0.9155 (mp) cc_final: 0.8901 (mp)
REVERT: N   13 ASN cc_start: 0.8893 (t0) cc_final: 0.8553 (t0)
REVERT: N   20 MET cc_start: 0.9079 (ttm) cc_final: 0.8661 (tmm)
REVERT: N   21 PHE cc_start: 0.9171 (m-10) cc_final: 0.8734 (m-80)
REVERT: P   12 MET cc_start: 0.9225 (mmp) cc_final: 0.7972 (mmp)
REVERT: P   58 PHE cc_start: 0.8895 (p90) cc_final: 0.8463 (p90)
REVERT: Q   21 LYS cc_start: 0.9461 (mmtt) cc_final: 0.9199 (pttt)
REVERT: Q   48 ASP cc_start: 0.8773 (t0) cc_final: 0.8302 (t0)
REVERT: Q   55 GLN cc_start: 0.9127 (mp10) cc_final: 0.8838 (mp-120)
REVERT: Q   88 GLU cc_start: 0.7302 (tp30) cc_final: 0.6899 (tp30)
REVERT: R   85 LYS cc_start: 0.9397 (tptp) cc_final: 0.9095 (tptp)
REVERT: R   86 GLN cc_start: 0.9221 (pm20) cc_final: 0.8679 (pp30)
REVERT: S   49 LYS cc_start: 0.9440 (tptt) cc_final: 0.9181 (tptt)
REVERT: S   99 ARG cc_start: 0.8673 (mpp-170) cc_final: 0.7658 (mpt180)
REVERT: S  103 ILE cc_start: 0.9693 (pt) cc_final: 0.9441 (mp)
REVERT: U    9 GLU cc_start: 0.8126 (tt0) cc_final: 0.7881 (tt0)
REVERT: Y    7 ARG cc_start: 0.8649 (ptt180) cc_final: 0.8424 (ptt90)
REVERT: Y   30 MET cc_start: 0.9086 (mmp) cc_final: 0.8791 (mmp)
REVERT: 0   14 MET cc_start: 0.9265 (mpp) cc_final: 0.9013 (mpp)
REVERT: 2   14 ARG cc_start: 0.8986 (mmt-90) cc_final: 0.8262 (mmp80)
REVERT: Z   20 LYS cc_start: 0.9423 (tptm) cc_final: 0.8996 (tptt)
REVERT: Z   24 LEU cc_start: 0.9614 (pp) cc_final: 0.9409 (pp)
REVERT: Z   46 MET cc_start: 0.8790 (mmp) cc_final: 0.8386 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2759
  time to fit residues: 95.0584
Evaluate side-chains
  161 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 120 optimal weight:   10.0000
   chunk 65 optimal weight:   20.0000
   chunk 229 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 80 optimal weight:   30.0000
   chunk 67 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 154 optimal weight:   30.0000
   chunk 231 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 41 optimal weight:   40.0000
   overall best weight:    9.3998

-------------------------------------------------------------------------------
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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.042521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.030210 restraints weight = 508494.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.031092 restraints weight = 229723.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.031616 restraints weight = 148376.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.031912 restraints weight = 117663.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.032041 restraints weight = 104223.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.7580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.105  48167  Z= 0.319
  Angle     :  0.759  11.164  72350  Z= 0.381
  Chirality :  0.040   0.269   9318
  Planarity :  0.006   0.078   3647
  Dihedral  : 24.958 178.224  24691
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 33.32
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.41 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.20), residues: 1569
  helix: -0.24 (0.23), residues: 476
  sheet: -2.09 (0.28), residues: 272
  loop : -1.70 (0.20), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Q  50 
 TYR   0.010   0.002   TYR N 112 
 PHE   0.019   0.002   PHE N  21 
 TRP   0.012   0.003   TRP R  92 
 HIS   0.007   0.002   HIS R  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 (48167)
  covalent geometry    : angle       0.75864 (72350)
  hydrogen bonds       : bond        0.11736 ( 1693)
  hydrogen bonds       : angle       4.26118 ( 3296)

*********************** 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
  199 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.870 
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: 0.8324 (ppp) cc_final: 0.8071 (ppp)
REVERT: E  124 PHE cc_start: 0.7393 (t80) cc_final: 0.7069 (t80)
REVERT: J   53 TYR cc_start: 0.9137 (m-80) cc_final: 0.8243 (m-80)
REVERT: J   67 ASN cc_start: 0.8717 (t0) cc_final: 0.8346 (t0)
REVERT: J   92 MET cc_start: 0.9679 (ttm) cc_final: 0.9111 (tpp)
REVERT: J  108 MET cc_start: 0.8229 (tpt) cc_final: 0.7882 (mmm)
REVERT: J  114 LEU cc_start: 0.8466 (mp) cc_final: 0.8121 (mp)
REVERT: K   79 PHE cc_start: 0.9350 (m-80) cc_final: 0.8867 (m-10)
REVERT: N   13 ASN cc_start: 0.8948 (t0) cc_final: 0.8609 (t0)
REVERT: N   20 MET cc_start: 0.9115 (ttm) cc_final: 0.8754 (tmm)
REVERT: N   21 PHE cc_start: 0.9173 (m-10) cc_final: 0.8737 (m-80)
REVERT: N   28 LEU cc_start: 0.9344 (tt) cc_final: 0.9128 (tp)
REVERT: P   12 MET cc_start: 0.9203 (mmp) cc_final: 0.8021 (mmp)
REVERT: P   58 PHE cc_start: 0.8934 (p90) cc_final: 0.8462 (p90)
REVERT: Q   21 LYS cc_start: 0.9462 (mmtt) cc_final: 0.9184 (pttt)
REVERT: R   15 SER cc_start: 0.9464 (t) cc_final: 0.9245 (p)
REVERT: R   45 GLU cc_start: 0.9042 (mp0) cc_final: 0.8830 (mp0)
REVERT: R   71 LYS cc_start: 0.9285 (tmtt) cc_final: 0.8774 (tptm)
REVERT: R   97 LYS cc_start: 0.9241 (tmmt) cc_final: 0.8811 (tmtt)
REVERT: S   49 LYS cc_start: 0.9447 (tptt) cc_final: 0.9200 (tptt)
REVERT: S   65 ASP cc_start: 0.8589 (t0) cc_final: 0.8199 (t0)
REVERT: S   66 ILE cc_start: 0.7769 (mm) cc_final: 0.7559 (mm)
REVERT: S  103 ILE cc_start: 0.9712 (pt) cc_final: 0.9463 (mp)
REVERT: S  109 ASP cc_start: 0.8099 (m-30) cc_final: 0.7752 (m-30)
REVERT: U    9 GLU cc_start: 0.8151 (tt0) cc_final: 0.7882 (tt0)
REVERT: Y    7 ARG cc_start: 0.8730 (ptt180) cc_final: 0.8476 (ptt90)
REVERT: Y   30 MET cc_start: 0.9102 (mmp) cc_final: 0.8771 (mmp)
REVERT: 0    6 LYS cc_start: 0.8991 (tttt) cc_final: 0.8615 (tttm)
REVERT: 0   11 LYS cc_start: 0.9507 (mmmm) cc_final: 0.8930 (mmmm)
REVERT: 0   14 MET cc_start: 0.9271 (mpp) cc_final: 0.8897 (mpp)
REVERT: 0   19 ASP cc_start: 0.8923 (m-30) cc_final: 0.8664 (m-30)
REVERT: 2   14 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8752 (mmt-90)
REVERT: Z   20 LYS cc_start: 0.9434 (tptm) cc_final: 0.9029 (tptt)
REVERT: Z   46 MET cc_start: 0.8769 (mmp) cc_final: 0.8461 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2740
  time to fit residues: 90.9454
Evaluate side-chains
  158 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 116 optimal weight:   10.0000
   chunk 127 optimal weight:   30.0000
   chunk 289 optimal weight:    5.9990
   chunk 80 optimal weight:   30.0000
   chunk 178 optimal weight:    8.9990
   chunk 174 optimal weight:    6.9990
   chunk 109 optimal weight:   20.0000
   chunk 237 optimal weight:   10.0000
   chunk 172 optimal weight:    4.9990
   chunk 234 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  18 GLN
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.043398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.030977 restraints weight = 501030.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.031914 restraints weight = 227125.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.032455 restraints weight = 146547.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.032747 restraints weight = 116058.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.032890 restraints weight = 102928.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.7506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  48167  Z= 0.236
  Angle     :  0.652   8.693  72350  Z= 0.329
  Chirality :  0.036   0.236   9318
  Planarity :  0.005   0.062   3647
  Dihedral  : 24.755 177.021  24691
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 26.26
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.14 %
    Favored  : 92.80 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.89 (0.20), residues: 1569
  helix: -0.14 (0.23), residues: 487
  sheet: -1.96 (0.28), residues: 277
  loop : -1.66 (0.20), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Y  29 
 TYR   0.016   0.002   TYR S  38 
 PHE   0.022   0.002   PHE D  90 
 TRP   0.010   0.002   TRP P  30 
 HIS   0.005   0.001   HIS R  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (48167)
  covalent geometry    : angle       0.65205 (72350)
  hydrogen bonds       : bond        0.09383 ( 1693)
  hydrogen bonds       : angle       4.01345 ( 3296)

*********************** 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
  206 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.8294 (ppp) cc_final: 0.8045 (ppp)
REVERT: E  188 MET cc_start: 0.8772 (ptm) cc_final: 0.8523 (ptm)
REVERT: J   53 TYR cc_start: 0.9115 (m-80) cc_final: 0.8182 (m-80)
REVERT: J   67 ASN cc_start: 0.8795 (t0) cc_final: 0.8350 (t0)
REVERT: J   92 MET cc_start: 0.9679 (ttm) cc_final: 0.9095 (tpp)
REVERT: J  114 LEU cc_start: 0.8617 (mp) cc_final: 0.8075 (mp)
REVERT: K   79 PHE cc_start: 0.9293 (m-80) cc_final: 0.8955 (m-10)
REVERT: N   13 ASN cc_start: 0.8800 (t0) cc_final: 0.8420 (t0)
REVERT: N   20 MET cc_start: 0.9106 (ttm) cc_final: 0.8687 (tmm)
REVERT: N   21 PHE cc_start: 0.9156 (m-10) cc_final: 0.8568 (m-80)
REVERT: P   12 MET cc_start: 0.9199 (mmp) cc_final: 0.8120 (mmm)
REVERT: P   58 PHE cc_start: 0.8887 (p90) cc_final: 0.8412 (p90)
REVERT: Q   21 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9201 (pttt)
REVERT: Q   48 ASP cc_start: 0.8704 (t0) cc_final: 0.8274 (t0)
REVERT: Q   55 GLN cc_start: 0.9108 (mp10) cc_final: 0.8872 (mp10)
REVERT: R   26 ASP cc_start: 0.9262 (p0) cc_final: 0.9044 (p0)
REVERT: R   45 GLU cc_start: 0.8947 (mp0) cc_final: 0.8727 (mp0)
REVERT: R   71 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8718 (tptm)
REVERT: R   85 LYS cc_start: 0.9370 (tptp) cc_final: 0.8824 (tptp)
REVERT: R   86 GLN cc_start: 0.9236 (pm20) cc_final: 0.8587 (pp30)
REVERT: R   97 LYS cc_start: 0.9104 (tmmt) cc_final: 0.8640 (tmtt)
REVERT: S    1 MET cc_start: 0.5741 (ptt) cc_final: 0.5190 (pmm)
REVERT: S   49 LYS cc_start: 0.9428 (tptt) cc_final: 0.9128 (tptm)
REVERT: S   65 ASP cc_start: 0.8669 (t0) cc_final: 0.8347 (t0)
REVERT: S   99 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8628 (mtm180)
REVERT: S  103 ILE cc_start: 0.9701 (pt) cc_final: 0.9452 (mp)
REVERT: U    9 GLU cc_start: 0.8147 (tt0) cc_final: 0.7880 (tt0)
REVERT: Y    7 ARG cc_start: 0.8748 (ptt180) cc_final: 0.8475 (ptt90)
REVERT: Y   30 MET cc_start: 0.8973 (mmp) cc_final: 0.8745 (mmp)
REVERT: 0    6 LYS cc_start: 0.8966 (tttt) cc_final: 0.8612 (tttm)
REVERT: 0   11 LYS cc_start: 0.9503 (mmmm) cc_final: 0.9262 (mmmm)
REVERT: 0   14 MET cc_start: 0.9276 (mpp) cc_final: 0.9007 (mpp)
REVERT: 0   19 ASP cc_start: 0.8966 (m-30) cc_final: 0.8652 (m-30)
REVERT: 2   14 ARG cc_start: 0.8930 (mmt-90) cc_final: 0.8718 (mmt-90)
REVERT: 2   22 MET cc_start: 0.8834 (tpp) cc_final: 0.8498 (mmm)
REVERT: Z   20 LYS cc_start: 0.9415 (tptm) cc_final: 0.8994 (tptt)
REVERT: Z   46 MET cc_start: 0.8812 (mmp) cc_final: 0.8489 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2750
  time to fit residues: 94.0301
Evaluate side-chains
  162 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 42 optimal weight:   30.0000
   chunk 153 optimal weight:    5.9990
   chunk 270 optimal weight:    9.9990
   chunk 195 optimal weight:    7.9990
   chunk 78 optimal weight:   20.0000
   chunk 71 optimal weight:   20.0000
   chunk 94 optimal weight:   10.0000
   chunk 128 optimal weight:   20.0000
   chunk 197 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 274 optimal weight:   30.0000
   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  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.042458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.030181 restraints weight = 512602.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.031076 restraints weight = 230701.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.031605 restraints weight = 148867.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.031893 restraints weight = 118260.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.031978 restraints weight = 105134.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.7959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  48167  Z= 0.299
  Angle     :  0.737  10.653  72350  Z= 0.370
  Chirality :  0.039   0.263   9318
  Planarity :  0.006   0.116   3647
  Dihedral  : 24.978 177.163  24691
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 32.82
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.92 %
    Favored  : 91.01 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.20), residues: 1569
  helix: -0.40 (0.22), residues: 486
  sheet: -2.24 (0.28), residues: 274
  loop : -1.76 (0.20), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.001   ARG L   2 
 TYR   0.018   0.002   TYR S  38 
 PHE   0.022   0.002   PHE Q  56 
 TRP   0.015   0.002   TRP E  78 
 HIS   0.009   0.002   HIS 0  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 (48167)
  covalent geometry    : angle       0.73691 (72350)
  hydrogen bonds       : bond        0.11350 ( 1693)
  hydrogen bonds       : angle       4.22419 ( 3296)

********************** 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
  199 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.8266 (ppp) cc_final: 0.8050 (ppp)
REVERT: D   90 PHE cc_start: 0.8552 (m-80) cc_final: 0.8282 (m-80)
REVERT: E    9 GLN cc_start: 0.9158 (mp-120) cc_final: 0.8934 (mp-120)
REVERT: E  124 PHE cc_start: 0.7659 (t80) cc_final: 0.7357 (t80)
REVERT: E  188 MET cc_start: 0.8824 (ptm) cc_final: 0.8543 (ptm)
REVERT: J   53 TYR cc_start: 0.9136 (m-80) cc_final: 0.8138 (m-80)
REVERT: J   67 ASN cc_start: 0.8747 (t0) cc_final: 0.8357 (t0)
REVERT: J   92 MET cc_start: 0.9659 (ttm) cc_final: 0.9080 (tpp)
REVERT: J  108 MET cc_start: 0.8146 (tpt) cc_final: 0.7834 (mmm)
REVERT: J  114 LEU cc_start: 0.8673 (mp) cc_final: 0.8127 (mp)
REVERT: K   65 THR cc_start: 0.9003 (p) cc_final: 0.8802 (p)
REVERT: K   79 PHE cc_start: 0.9292 (m-80) cc_final: 0.8940 (m-10)
REVERT: K   82 ASN cc_start: 0.8508 (p0) cc_final: 0.8190 (p0)
REVERT: N   10 LEU cc_start: 0.9163 (mp) cc_final: 0.8908 (mp)
REVERT: N   13 ASN cc_start: 0.8843 (t0) cc_final: 0.8634 (t0)
REVERT: N   20 MET cc_start: 0.9071 (ttm) cc_final: 0.8695 (tmm)
REVERT: N   21 PHE cc_start: 0.9144 (m-10) cc_final: 0.8583 (m-80)
REVERT: P   12 MET cc_start: 0.9168 (mmp) cc_final: 0.8097 (mmm)
REVERT: P   58 PHE cc_start: 0.8855 (p90) cc_final: 0.8389 (p90)
REVERT: Q   21 LYS cc_start: 0.9471 (mmtt) cc_final: 0.9139 (mmmt)
REVERT: Q   55 GLN cc_start: 0.9146 (mp10) cc_final: 0.8898 (mp10)
REVERT: R   26 ASP cc_start: 0.9244 (p0) cc_final: 0.8979 (p0)
REVERT: R   71 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8696 (tptm)
REVERT: R   85 LYS cc_start: 0.9341 (tptp) cc_final: 0.9087 (tptp)
REVERT: S   49 LYS cc_start: 0.9422 (tptt) cc_final: 0.9119 (tptm)
REVERT: S   65 ASP cc_start: 0.8661 (t0) cc_final: 0.8310 (t0)
REVERT: S   99 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8612 (mtm180)
REVERT: S  103 ILE cc_start: 0.9709 (pt) cc_final: 0.9452 (mp)
REVERT: S  109 ASP cc_start: 0.8032 (m-30) cc_final: 0.7820 (m-30)
REVERT: U    9 GLU cc_start: 0.8082 (tt0) cc_final: 0.7830 (tt0)
REVERT: U   52 ASN cc_start: 0.8344 (t0) cc_final: 0.8130 (t0)
REVERT: Y   29 ARG cc_start: 0.8244 (ptt-90) cc_final: 0.7697 (ptt-90)
REVERT: 0    6 LYS cc_start: 0.8993 (tttt) cc_final: 0.8617 (tttm)
REVERT: 0   11 LYS cc_start: 0.9504 (mmmm) cc_final: 0.8932 (mmmm)
REVERT: 0   14 MET cc_start: 0.9262 (mpp) cc_final: 0.8862 (mpp)
REVERT: 0   19 ASP cc_start: 0.8968 (m-30) cc_final: 0.8672 (m-30)
REVERT: 2   14 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8725 (mmt-90)
REVERT: 2   22 MET cc_start: 0.8871 (tpp) cc_final: 0.8571 (mmm)
REVERT: Z   20 LYS cc_start: 0.9441 (tptm) cc_final: 0.9017 (tptt)
REVERT: Z   24 LEU cc_start: 0.9617 (pp) cc_final: 0.9391 (pp)
REVERT: Z   46 MET cc_start: 0.8809 (mmp) cc_final: 0.8538 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2688
  time to fit residues: 89.6519
Evaluate side-chains
  162 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 301
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 217 optimal weight:   50.0000
   chunk 201 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 107 optimal weight:   30.0000
   chunk 180 optimal weight:    5.9990
   chunk 229 optimal weight:    3.9990
   chunk 131 optimal weight:   40.0000
   chunk 181 optimal weight:    7.9990
   chunk 289 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   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  94 GLN
** E  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K   3 GLN
K  29 HIS
L   4 ASN
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
2  26 ASN
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.043199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.030843 restraints weight = 510063.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.031784 restraints weight = 228593.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 73)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.032310 restraints weight = 146830.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.032615 restraints weight = 116501.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.032701 restraints weight = 103106.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.7925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  48167  Z= 0.240
  Angle     :  0.656  10.067  72350  Z= 0.331
  Chirality :  0.036   0.232   9318
  Planarity :  0.005   0.081   3647
  Dihedral  : 24.835 177.136  24691
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 27.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.46 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.20), residues: 1569
  helix: -0.16 (0.23), residues: 481
  sheet: -2.18 (0.27), residues: 293
  loop : -1.75 (0.20), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L   2 
 TYR   0.012   0.002   TYR J  16 
 PHE   0.019   0.002   PHE Q  56 
 TRP   0.010   0.002   TRP R  92 
 HIS   0.011   0.001   HIS K  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (48167)
  covalent geometry    : angle       0.65614 (72350)
  hydrogen bonds       : bond        0.09582 ( 1693)
  hydrogen bonds       : angle       4.04160 ( 3296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7502.57 seconds
wall clock time: 132 minutes 8.03 seconds (7928.03 seconds total)