Starting phenix.real_space_refine
on Mon Aug 10 05:59:32 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_16503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_16503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_16503.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_16503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_16503.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_16503.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8c96_16503/08_2026/8c96_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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 7.85, per 1000 atoms: 0.18
  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: 3.31
  Conformation dependent library (CDL) restraints added in 826.2 milliseconds
  

  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: 5.82
  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: 19.85

  Time building geometry restraints manager: 4.64 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
    1.478  1.574 -0.096 2.00e-02 2.50e+03 2.29e+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: 65082
        1.16 -     2.31: 3379
        2.31 -     3.47: 3201
        3.47 -     4.62: 464
        4.62 -     5.78: 224
  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
     119.70  123.80   -4.10 1.20e+00 6.94e-01 1.16e+01
  angle pdb=" C3'   G A  51 "
        pdb=" C2'   G A  51 "
        pdb=" O2'   G A  51 "
      ideal   model   delta    sigma   weight residual
     109.80  115.10   -5.30 2.00e+00 2.50e-01 7.03e+00
  angle pdb=" C3'   G A 301 "
        pdb=" C2'   G A 301 "
        pdb=" O2'   G A 301 "
      ideal   model   delta    sigma   weight residual
     109.80  115.02   -5.22 2.00e+00 2.50e-01 6.80e+00
  angle pdb=" C3'   A A1301 "
        pdb=" C2'   A A1301 "
        pdb=" O2'   A A1301 "
      ideal   model   delta    sigma   weight residual
     109.80  115.01   -5.21 2.00e+00 2.50e-01 6.78e+00
  angle pdb=" C3'   A A1652 "
        pdb=" O3'   A A1652 "
        pdb=" P     G A1653 "
      ideal   model   delta    sigma   weight residual
     119.70  122.79   -3.09 1.20e+00 6.94e-01 6.65e+00
  ... (remaining 72345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.99: 22807
       34.99 -    69.98: 2467
       69.98 -   104.96: 233
      104.96 -   139.95: 1
      139.95 -   174.94: 3
  Dihedral angle restraints: 25511
    sinusoidal: 20950
      harmonic: 4561
  Sorted by residual:
  dihedral pdb=" C4'   G A 215 "
           pdb=" C3'   G A 215 "
           pdb=" C2'   G A 215 "
           pdb=" C1'   G A 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.44   73.78     1      3.10e+00 1.04e-01 7.20e+02
  dihedral pdb=" C4'   U A 395 "
           pdb=" C3'   U A 395 "
           pdb=" C2'   U A 395 "
           pdb=" C1'   U A 395 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.01   73.35     1      3.10e+00 1.04e-01 7.13e+02
  dihedral pdb=" C4'   U A2728 "
           pdb=" C3'   U A2728 "
           pdb=" C2'   U A2728 "
           pdb=" C1'   U A2728 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.95   73.29     1      3.10e+00 1.04e-01 7.12e+02
  ... (remaining 25508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 5942
       0.064 -    0.128: 1457
       0.128 -    0.192: 18
       0.192 -    0.256: 1649
       0.256 -    0.319: 252
  Chirality restraints: 9318
  Sorted by residual:
  chirality pdb=" P     A A 272 "
            pdb=" OP1   A A 272 "
            pdb=" OP2   A A 272 "
            pdb=" O5'   A A 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.49   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" P     G A1653 "
            pdb=" OP1   G A1653 "
            pdb=" OP2   G A1653 "
            pdb=" O5'   G A1653 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.49   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" P     G A1236 "
            pdb=" OP1   G A1236 "
            pdb=" OP2   G A1236 "
            pdb=" O5'   G A1236 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.46   -0.29 2.00e-01 2.50e+01 2.11e+00
  ... (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:             2.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.040
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     48.920
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
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      :  0.003   0.096  48167  Z= 0.128
  Angle     :  0.841   5.780  72350  Z= 0.342
  Chirality :  0.114   0.319   9318
  Planarity :  0.002   0.029   3647
  Dihedral  : 20.411 174.940  22563
  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 are 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/Z
  covalent geometry    : bond        0.00256 /  0.13 (48167)
  covalent geometry    : angle       0.84079 /  0.34 (72350)
  hydrogen bonds       : bond        0.09920 /  5.16 ( 1693)
  hydrogen bonds       : angle       4.12062 /  1.72 ( 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  : 0.872 
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: 0.2536
  time to fit residues: 128.1572
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  : 0.856 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 261 optimal weight:    7.9990
   chunk 248 optimal weight:    8.9990
   chunk 207 optimal weight:    0.9980
   chunk 155 optimal weight:    6.9990
   chunk 244 optimal weight:    0.9980
   chunk 183 optimal weight:    0.6980
   chunk 298 optimal weight:    8.9990
   overall best weight:    3.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 HIS
D 173 GLN
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 132 HIS
N  18 GLN
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
** 2  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.053800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.041059 restraints weight = 482356.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.041984 restraints weight = 221753.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.042605 restraints weight = 141301.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.042939 restraints weight = 110973.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.043133 restraints weight = 98140.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  48167  Z= 0.211
  Angle     :  1.217  17.072  72350  Z= 0.486
  Chirality :  0.098   1.128   9318
  Planarity :  0.005   0.071   3647
  Dihedral  : 19.750 179.608  19449
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.68 %
    Favored  : 97.25 %
  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 are not related in a simple way.
  whole: -0.01 (0.21), residues: 1569
  helix:  1.29 (0.24), residues: 477
  sheet: -0.02 (0.32), residues: 257
  loop : -0.76 (0.21), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Z  44 
 TYR   0.011   0.001   TYR N 112 
 PHE   0.022   0.001   PHE N  21 
 TRP   0.025   0.003   TRP E  78 
 HIS   0.003   0.001   HIS R  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.21 (48167)
  covalent geometry    : angle       1.21708 /  0.49 (72350)
  hydrogen bonds       : bond        0.07457 /  3.84 ( 1693)
  hydrogen bonds       : angle       3.64862 /  1.55 ( 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
  261 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 260
  time to evaluate  : 0.788 
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   19 PHE cc_start: 0.7815 (m-80) cc_final: 0.7602 (m-80)
REVERT: E   41 GLN cc_start: 0.8606 (tp40) cc_final: 0.8170 (tp40)
REVERT: E  115 GLN cc_start: 0.9133 (tp40) cc_final: 0.8655 (tm-30)
REVERT: E  188 MET cc_start: 0.8850 (ptm) cc_final: 0.8607 (ptm)
REVERT: J   53 TYR cc_start: 0.8422 (m-10) cc_final: 0.7867 (m-80)
REVERT: J   67 ASN cc_start: 0.7450 (t0) cc_final: 0.6995 (t0)
REVERT: J   74 TYR cc_start: 0.7760 (m-10) cc_final: 0.7454 (m-10)
REVERT: J   92 MET cc_start: 0.9510 (ttm) cc_final: 0.9032 (tpt)
REVERT: J  125 TYR cc_start: 0.6779 (m-10) cc_final: 0.6507 (m-10)
REVERT: K    3 GLN cc_start: 0.5996 (pm20) cc_final: 0.5324 (pm20)
REVERT: K    7 MET cc_start: 0.7902 (tpt) cc_final: 0.6931 (tmm)
REVERT: K   20 MET cc_start: 0.8437 (tmm) cc_final: 0.8213 (tmm)
REVERT: K   58 LEU cc_start: 0.7078 (tp) cc_final: 0.6645 (tp)
REVERT: K   79 PHE cc_start: 0.9280 (m-80) cc_final: 0.8710 (m-80)
REVERT: N   13 ASN cc_start: 0.8985 (m-40) cc_final: 0.8656 (m-40)
REVERT: N   20 MET cc_start: 0.8961 (ttm) cc_final: 0.8379 (tmm)
REVERT: P   73 PHE cc_start: 0.7805 (m-80) cc_final: 0.7338 (m-80)
REVERT: Q   36 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8483 (tm-30)
REVERT: Q   48 ASP cc_start: 0.8155 (t0) cc_final: 0.7530 (t0)
REVERT: R   27 ILE cc_start: 0.8212 (mm) cc_final: 0.7722 (mm)
REVERT: R   31 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: R   70 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7147 (tm-30)
REVERT: R   78 ARG cc_start: 0.8894 (tpt-90) cc_final: 0.8669 (tpt-90)
REVERT: R   85 LYS cc_start: 0.9244 (tttp) cc_final: 0.9029 (tttp)
REVERT: R   86 GLN cc_start: 0.7687 (pp30) cc_final: 0.7455 (pp30)
REVERT: R   87 GLN cc_start: 0.8170 (pp30) cc_final: 0.7248 (pp30)
REVERT: S   49 LYS cc_start: 0.9506 (tptt) cc_final: 0.8799 (tptt)
REVERT: S   68 ASP cc_start: 0.8021 (p0) cc_final: 0.7683 (p0)
REVERT: S   99 ARG cc_start: 0.8207 (mpt180) cc_final: 0.7617 (mpt180)
REVERT: S  103 ILE cc_start: 0.9535 (pt) cc_final: 0.9172 (mp)
REVERT: Y    1 MET cc_start: 0.8054 (ppp) cc_final: 0.7239 (ppp)
REVERT: Y   29 ARG cc_start: 0.8249 (ptt-90) cc_final: 0.7672 (ptt-90)
REVERT: Y   30 MET cc_start: 0.8754 (mmp) cc_final: 0.8518 (mmm)
REVERT: Y   45 GLN cc_start: 0.9387 (tt0) cc_final: 0.9180 (tm-30)
REVERT: 0   16 ARG cc_start: 0.9382 (mtt180) cc_final: 0.8684 (mtt90)
REVERT: 2   14 ARG cc_start: 0.8122 (mmp80) cc_final: 0.7261 (mmp80)
REVERT: Z   20 LYS cc_start: 0.9312 (tptm) cc_final: 0.8881 (tptt)
REVERT: Z   53 MET cc_start: 0.7904 (mmt) cc_final: 0.7404 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2505
  time to fit residues: 107.4291
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  : 0.564 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 83 optimal weight:    9.9990
   chunk 158 optimal weight:   20.0000
   chunk 204 optimal weight:   10.0000
   chunk 256 optimal weight:   20.0000
   chunk 131 optimal weight:   30.0000
   chunk 106 optimal weight:   30.0000
   chunk 66 optimal weight:   10.0000
   chunk 172 optimal weight:    8.9990
   chunk 238 optimal weight:   30.0000
   overall best weight:    8.9994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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**
D 164 GLN
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 135 GLN
K  29 HIS
** N  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 HIS
N 107 ASN
P  65 ASN
** R  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U  44 HIS
U  68 ASN
Y  20 ASN
** 2  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3287 r_free = 0.3287 target = 0.045838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.033132 restraints weight = 511346.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.034117 restraints weight = 234125.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.034688 restraints weight = 152570.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.034968 restraints weight = 120932.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.035087 restraints weight = 107880.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.087  48167  Z= 0.351
  Angle     :  1.303  14.040  72350  Z= 0.526
  Chirality :  0.085   1.029   9318
  Planarity :  0.007   0.110   3647
  Dihedral  : 20.489 179.248  19449
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 31.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.65 %
    Favored  : 93.12 %
  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 are not related in a simple way.
  whole: -1.05 (0.20), residues: 1569
  helix:  0.19 (0.22), residues: 488
  sheet: -0.58 (0.30), residues: 278
  loop : -1.27 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.001   ARG R  21 
 TYR   0.014   0.002   TYR J  53 
 PHE   0.023   0.003   PHE N 102 
 TRP   0.033   0.004   TRP R  92 
 HIS   0.015   0.002   HIS N   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00697 /  0.35 (48167)
  covalent geometry    : angle       1.30317 /  0.53 (72350)
  hydrogen bonds       : bond        0.12979 /  6.75 ( 1693)
  hydrogen bonds       : angle       4.34380 /  1.83 ( 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
  230 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 227
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  188 MET cc_start: 0.8799 (ptm) cc_final: 0.8502 (ptm)
REVERT: J   53 TYR cc_start: 0.9013 (m-80) cc_final: 0.8298 (m-80)
REVERT: J   67 ASN cc_start: 0.8621 (t0) cc_final: 0.8105 (t0)
REVERT: J   74 TYR cc_start: 0.8113 (m-10) cc_final: 0.7817 (m-10)
REVERT: J   92 MET cc_start: 0.9535 (ttm) cc_final: 0.9160 (tpt)
REVERT: K    1 MET cc_start: 0.6430 (tmm) cc_final: 0.3872 (ptp)
REVERT: K    7 MET cc_start: 0.7835 (tpt) cc_final: 0.7500 (tmm)
REVERT: K   58 LEU cc_start: 0.6887 (tp) cc_final: 0.6489 (tp)
REVERT: K   79 PHE cc_start: 0.9161 (m-80) cc_final: 0.8526 (m-80)
REVERT: K  110 GLU cc_start: 0.5837 (mp0) cc_final: 0.5564 (mp0)
REVERT: N   20 MET cc_start: 0.9007 (ttm) cc_final: 0.8740 (mtt)
REVERT: P    9 GLN cc_start: 0.8676 (mp-120) cc_final: 0.8405 (mm-40)
REVERT: P   58 PHE cc_start: 0.8946 (p90) cc_final: 0.8709 (p90)
REVERT: R   83 TYR cc_start: 0.8043 (t80) cc_final: 0.7842 (t80)
REVERT: S   38 TYR cc_start: 0.8630 (m-10) cc_final: 0.8229 (m-10)
REVERT: S   68 ASP cc_start: 0.8186 (p0) cc_final: 0.7810 (p0)
REVERT: S  103 ILE cc_start: 0.9677 (pt) cc_final: 0.9369 (mp)
REVERT: Y    1 MET cc_start: 0.8126 (ppp) cc_final: 0.7362 (ppp)
REVERT: Y    7 ARG cc_start: 0.8688 (ptt180) cc_final: 0.8069 (ptt180)
REVERT: Y   30 MET cc_start: 0.8949 (mmp) cc_final: 0.8693 (mmm)
REVERT: 0    6 LYS cc_start: 0.9069 (tttt) cc_final: 0.8210 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9446 (mmmm) cc_final: 0.9130 (mmmm)
REVERT: Z   20 LYS cc_start: 0.9409 (tptm) cc_final: 0.8976 (tptp)
REVERT: Z   51 SER cc_start: 0.9158 (p) cc_final: 0.8754 (m)
  outliers start: 3
  outliers final: 1
  residues processed: 230
  average time/residue: 0.2365
  time to fit residues: 90.5967
Evaluate side-chains
  174 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 177 optimal weight:    9.9990
   chunk 16 optimal weight:   30.0000
   chunk 162 optimal weight:   10.0000
   chunk 203 optimal weight:    0.0670
   chunk 242 optimal weight:    7.9990
   chunk 212 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   chunk 293 optimal weight:    0.0270
   chunk 200 optimal weight:   20.0000
   chunk 281 optimal weight:    5.9990
   overall best weight:    4.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  89 ASN
N 107 ASN
P   9 GLN
P  65 ASN
R  11 GLN
R  86 GLN
U  52 ASN
** Y  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
2  13 ASN
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.047419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.034701 restraints weight = 489848.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.035747 restraints weight = 220880.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.036341 restraints weight = 141433.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.036673 restraints weight = 111173.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.036812 restraints weight = 97882.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.5475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  48167  Z= 0.215
  Angle     :  1.059  11.972  72350  Z= 0.426
  Chirality :  0.076   0.787   9318
  Planarity :  0.005   0.069   3647
  Dihedral  : 20.110 178.050  19449
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 20.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.36 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.20), residues: 1569
  helix:  0.59 (0.23), residues: 488
  sheet: -0.96 (0.28), residues: 297
  loop : -1.28 (0.21), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  17 
 TYR   0.011   0.002   TYR N 112 
 PHE   0.015   0.002   PHE Q  56 
 TRP   0.016   0.002   TRP P  30 
 HIS   0.006   0.001   HIS E  29 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.22 (48167)
  covalent geometry    : angle       1.05885 /  0.43 (72350)
  hydrogen bonds       : bond        0.08468 /  4.41 ( 1693)
  hydrogen bonds       : angle       3.79936 /  1.59 ( 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
  237 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 235
  time to evaluate  : 0.867 
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: D   38 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7977 (mmtt)
REVERT: E    1 MET cc_start: 0.7794 (pmm) cc_final: 0.7504 (pmm)
REVERT: E  188 MET cc_start: 0.8781 (ptm) cc_final: 0.8396 (ptm)
REVERT: J   53 TYR cc_start: 0.9135 (m-80) cc_final: 0.8380 (m-80)
REVERT: J   67 ASN cc_start: 0.8650 (t0) cc_final: 0.8102 (t0)
REVERT: J   71 ASP cc_start: 0.8120 (m-30) cc_final: 0.7349 (m-30)
REVERT: J   93 ILE cc_start: 0.9242 (pt) cc_final: 0.9035 (pt)
REVERT: K    1 MET cc_start: 0.6368 (tmm) cc_final: 0.4731 (ppp)
REVERT: K   58 LEU cc_start: 0.6616 (tp) cc_final: 0.6273 (tp)
REVERT: K   79 PHE cc_start: 0.9252 (m-80) cc_final: 0.8710 (m-80)
REVERT: N   10 LEU cc_start: 0.9106 (mp) cc_final: 0.8898 (mp)
REVERT: N   20 MET cc_start: 0.9200 (ttm) cc_final: 0.8723 (tmm)
REVERT: N   21 PHE cc_start: 0.9151 (m-80) cc_final: 0.8630 (m-80)
REVERT: P   12 MET cc_start: 0.9175 (mmp) cc_final: 0.7742 (mmm)
REVERT: P   58 PHE cc_start: 0.8907 (p90) cc_final: 0.8641 (p90)
REVERT: Q   31 TYR cc_start: 0.8277 (t80) cc_final: 0.7953 (t80)
REVERT: Q   61 ILE cc_start: 0.9529 (pt) cc_final: 0.9172 (mt)
REVERT: R   70 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: R   71 LYS cc_start: 0.9118 (tmtt) cc_final: 0.8703 (tptp)
REVERT: R   73 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8393 (mmtm)
REVERT: R   85 LYS cc_start: 0.9453 (tmtt) cc_final: 0.8902 (tptp)
REVERT: R   87 GLN cc_start: 0.8775 (pp30) cc_final: 0.7939 (pp30)
REVERT: R   97 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8920 (tptp)
REVERT: S   52 GLU cc_start: 0.8661 (pp20) cc_final: 0.8381 (tm-30)
REVERT: S   53 SER cc_start: 0.9448 (p) cc_final: 0.9240 (p)
REVERT: S   68 ASP cc_start: 0.7994 (p0) cc_final: 0.7619 (p0)
REVERT: S   99 ARG cc_start: 0.8570 (mpt180) cc_final: 0.8038 (mpt180)
REVERT: S  103 ILE cc_start: 0.9650 (pt) cc_final: 0.9448 (mp)
REVERT: Y    1 MET cc_start: 0.8201 (ppp) cc_final: 0.7482 (ppp)
REVERT: Y   18 LEU cc_start: 0.8849 (pp) cc_final: 0.8642 (tp)
REVERT: Y   29 ARG cc_start: 0.8477 (ptt-90) cc_final: 0.7902 (ptt-90)
REVERT: Y   30 MET cc_start: 0.8995 (mmp) cc_final: 0.8627 (mmp)
REVERT: 0    6 LYS cc_start: 0.9000 (tttt) cc_final: 0.8172 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9059 (mmmm)
REVERT: 0   14 MET cc_start: 0.9112 (mpp) cc_final: 0.8857 (mpp)
REVERT: Z   51 SER cc_start: 0.9167 (p) cc_final: 0.8767 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 236
  average time/residue: 0.2525
  time to fit residues: 99.5064
Evaluate side-chains
  181 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 215 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   chunk 189 optimal weight:    4.9990
   chunk 252 optimal weight:   10.0000
   chunk 264 optimal weight:   20.0000
   chunk 277 optimal weight:   30.0000
   chunk 3 optimal weight:   10.0000
   chunk 285 optimal weight:    0.6980
   chunk 183 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   overall best weight:    6.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  65 ASN
** R  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
Y  20 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.045733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.033105 restraints weight = 504347.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.034104 restraints weight = 231945.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.034669 restraints weight = 151316.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.034904 restraints weight = 120498.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.035090 restraints weight = 109200.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.6236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  48167  Z= 0.267
  Angle     :  1.124  12.543  72350  Z= 0.451
  Chirality :  0.077   0.900   9318
  Planarity :  0.005   0.066   3647
  Dihedral  : 20.184 178.989  19449
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 26.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.13 %
    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 are not related in a simple way.
  whole: -1.14 (0.20), residues: 1569
  helix:  0.39 (0.23), residues: 485
  sheet: -1.12 (0.28), residues: 284
  loop : -1.32 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R  21 
 TYR   0.014   0.002   TYR S  38 
 PHE   0.018   0.002   PHE N  21 
 TRP   0.017   0.002   TRP R  92 
 HIS   0.007   0.002   HIS N  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00536 /  0.27 (48167)
  covalent geometry    : angle       1.12441 /  0.45 (72350)
  hydrogen bonds       : bond        0.10299 /  5.39 ( 1693)
  hydrogen bonds       : angle       3.95350 /  1.67 ( 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
  216 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7793 (ppp) cc_final: 0.7570 (ppp)
REVERT: J   53 TYR cc_start: 0.8914 (m-80) cc_final: 0.8353 (m-80)
REVERT: J   67 ASN cc_start: 0.8645 (t0) cc_final: 0.8066 (t0)
REVERT: J   74 TYR cc_start: 0.8072 (m-10) cc_final: 0.7704 (m-10)
REVERT: J   92 MET cc_start: 0.9606 (ttm) cc_final: 0.9127 (tpp)
REVERT: K    1 MET cc_start: 0.5745 (tmm) cc_final: 0.4591 (pmm)
REVERT: K   65 THR cc_start: 0.9005 (p) cc_final: 0.8799 (p)
REVERT: K   79 PHE cc_start: 0.9246 (m-80) cc_final: 0.8773 (m-10)
REVERT: N   13 ASN cc_start: 0.8759 (t0) cc_final: 0.8451 (t0)
REVERT: N   20 MET cc_start: 0.9129 (ttm) cc_final: 0.8644 (tmm)
REVERT: N   21 PHE cc_start: 0.9135 (m-80) cc_final: 0.8822 (m-80)
REVERT: P   12 MET cc_start: 0.9252 (mmp) cc_final: 0.7749 (mmp)
REVERT: P   58 PHE cc_start: 0.8903 (p90) cc_final: 0.8574 (p90)
REVERT: Q   31 TYR cc_start: 0.8289 (t80) cc_final: 0.8000 (t80)
REVERT: Q   61 ILE cc_start: 0.9557 (pt) cc_final: 0.9227 (mt)
REVERT: R   70 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: R   71 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8797 (tptm)
REVERT: R   85 LYS cc_start: 0.9468 (tmtt) cc_final: 0.9082 (tptp)
REVERT: R   97 LYS cc_start: 0.9447 (tmtt) cc_final: 0.9143 (tptp)
REVERT: S   49 LYS cc_start: 0.9435 (tptt) cc_final: 0.9206 (tptt)
REVERT: S   68 ASP cc_start: 0.8049 (p0) cc_final: 0.7812 (p0)
REVERT: S  103 ILE cc_start: 0.9641 (pt) cc_final: 0.9436 (mp)
REVERT: U    9 GLU cc_start: 0.7903 (tt0) cc_final: 0.7351 (tt0)
REVERT: Y    7 ARG cc_start: 0.8781 (ptt180) cc_final: 0.8210 (ptt180)
REVERT: Y   13 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8278 (mp0)
REVERT: Y   30 MET cc_start: 0.9018 (mmp) cc_final: 0.8727 (mmp)
REVERT: 0    6 LYS cc_start: 0.8975 (tttt) cc_final: 0.8183 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9394 (mmmm) cc_final: 0.8725 (mmmm)
REVERT: 0   14 MET cc_start: 0.9206 (mpp) cc_final: 0.8885 (mpp)
REVERT: Z   20 LYS cc_start: 0.9410 (tptm) cc_final: 0.8974 (tptt)
REVERT: Z   24 LEU cc_start: 0.9624 (pp) cc_final: 0.9422 (pp)
REVERT: Z   46 MET cc_start: 0.8650 (mmp) cc_final: 0.8209 (mmp)
REVERT: Z   51 SER cc_start: 0.9166 (p) cc_final: 0.8742 (m)
REVERT: Z   53 MET cc_start: 0.8507 (mmt) cc_final: 0.7988 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.2646
  time to fit residues: 94.7449
Evaluate side-chains
  164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 33 optimal weight:    9.9990
   chunk 226 optimal weight:   20.0000
   chunk 118 optimal weight:    9.9990
   chunk 285 optimal weight:   10.0000
   chunk 75 optimal weight:   30.0000
   chunk 255 optimal weight:    6.9990
   chunk 76 optimal weight:    9.9990
   chunk 145 optimal weight:   20.0000
   chunk 168 optimal weight:    6.9990
   chunk 240 optimal weight:   20.0000
   overall best weight:    8.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 107 ASN
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  55 GLN
Q  80 ASN
R  12 HIS
R  43 ASN
U  44 HIS
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
0   5 ASN
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.043794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.031357 restraints weight = 520271.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.032304 restraints weight = 237773.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.032845 restraints weight = 154328.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.033156 restraints weight = 122900.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.033263 restraints weight = 108708.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.7445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.128  48167  Z= 0.332
  Angle     :  1.244  14.518  72350  Z= 0.499
  Chirality :  0.083   0.919   9318
  Planarity :  0.006   0.082   3647
  Dihedral  : 20.606 178.646  19449
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 31.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.52 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.20), residues: 1569
  helix: -0.13 (0.22), residues: 479
  sheet: -1.32 (0.28), residues: 284
  loop : -1.54 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG Q  50 
 TYR   0.016   0.002   TYR N 112 
 PHE   0.024   0.003   PHE N  21 
 TRP   0.017   0.002   TRP R  92 
 HIS   0.010   0.002   HIS N   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00669 /  0.33 (48167)
  covalent geometry    : angle       1.24424 /  0.50 (72350)
  hydrogen bonds       : bond        0.11685 /  6.11 ( 1693)
  hydrogen bonds       : angle       4.26428 /  1.79 ( 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
  200 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.833 
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: J   53 TYR cc_start: 0.9026 (m-80) cc_final: 0.8198 (m-80)
REVERT: J   67 ASN cc_start: 0.8528 (t0) cc_final: 0.8086 (t0)
REVERT: J   92 MET cc_start: 0.9619 (ttm) cc_final: 0.9121 (tpp)
REVERT: K    1 MET cc_start: 0.5415 (tmm) cc_final: 0.4529 (pmm)
REVERT: K   65 THR cc_start: 0.9028 (p) cc_final: 0.8801 (p)
REVERT: K   79 PHE cc_start: 0.9339 (m-80) cc_final: 0.8770 (m-10)
REVERT: K   87 LEU cc_start: 0.7001 (mp) cc_final: 0.6786 (mp)
REVERT: K  110 GLU cc_start: 0.6171 (mp0) cc_final: 0.5969 (mp0)
REVERT: L   17 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8490 (mmmm)
REVERT: L   81 ASP cc_start: 0.8177 (t70) cc_final: 0.6835 (m-30)
REVERT: N   13 ASN cc_start: 0.8816 (t0) cc_final: 0.8515 (t0)
REVERT: N   20 MET cc_start: 0.9107 (ttm) cc_final: 0.8745 (tmm)
REVERT: N   21 PHE cc_start: 0.9245 (m-10) cc_final: 0.8799 (m-80)
REVERT: N  110 MET cc_start: 0.8628 (mpp) cc_final: 0.8297 (mpp)
REVERT: P   12 MET cc_start: 0.9173 (mmp) cc_final: 0.7943 (mmp)
REVERT: P   58 PHE cc_start: 0.8893 (p90) cc_final: 0.8468 (p90)
REVERT: Q   21 LYS cc_start: 0.9503 (mmtt) cc_final: 0.9185 (pttt)
REVERT: Q   61 ILE cc_start: 0.9575 (pt) cc_final: 0.9211 (mt)
REVERT: R   71 LYS cc_start: 0.9116 (tmtt) cc_final: 0.8896 (tptm)
REVERT: S   68 ASP cc_start: 0.7868 (p0) cc_final: 0.7626 (p0)
REVERT: S   82 MET cc_start: 0.7377 (tpp) cc_final: 0.7131 (tpp)
REVERT: S  103 ILE cc_start: 0.9703 (pt) cc_final: 0.9410 (mp)
REVERT: U    9 GLU cc_start: 0.8073 (tt0) cc_final: 0.7832 (tt0)
REVERT: Y    1 MET cc_start: 0.8346 (ppp) cc_final: 0.8118 (ppp)
REVERT: Y   30 MET cc_start: 0.9053 (mmp) cc_final: 0.8728 (mmp)
REVERT: 0    6 LYS cc_start: 0.8899 (tttt) cc_final: 0.8089 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9429 (mmmm) cc_final: 0.8742 (mmmm)
REVERT: 0   14 MET cc_start: 0.9246 (mpp) cc_final: 0.8808 (mpp)
REVERT: 0   19 ASP cc_start: 0.8855 (m-30) cc_final: 0.8609 (m-30)
REVERT: 2   14 ARG cc_start: 0.8976 (mmt-90) cc_final: 0.8482 (mmp80)
REVERT: Z   20 LYS cc_start: 0.9440 (tptm) cc_final: 0.9005 (tptt)
REVERT: Z   24 LEU cc_start: 0.9646 (pp) cc_final: 0.9411 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2463
  time to fit residues: 81.6867
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  : 0.794 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 189 optimal weight:   20.0000
   chunk 286 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 102 optimal weight:   10.0000
   chunk 296 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 150 optimal weight:   10.0000
   chunk 152 optimal weight:    0.9980
   chunk 197 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   overall best weight:    7.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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**
** J  47 HIS ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.044303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.031874 restraints weight = 513728.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.032841 restraints weight = 235622.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.033387 restraints weight = 152889.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.033705 restraints weight = 121553.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.033841 restraints weight = 107529.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.7565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  48167  Z= 0.290
  Angle     :  1.161  13.546  72350  Z= 0.466
  Chirality :  0.080   0.887   9318
  Planarity :  0.005   0.078   3647
  Dihedral  : 20.453 177.772  19449
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 28.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.20), residues: 1569
  helix: -0.02 (0.23), residues: 480
  sheet: -1.57 (0.29), residues: 254
  loop : -1.51 (0.20), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Y  23 
 TYR   0.014   0.002   TYR Q  31 
 PHE   0.032   0.002   PHE D  90 
 TRP   0.026   0.003   TRP P  30 
 HIS   0.006   0.001   HIS R  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00583 /  0.29 (48167)
  covalent geometry    : angle       1.16071 /  0.47 (72350)
  hydrogen bonds       : bond        0.10437 /  5.46 ( 1693)
  hydrogen bonds       : angle       4.08687 /  1.71 ( 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
  210 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.742 
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: 0.8011 (ppp) cc_final: 0.7720 (ppp)
REVERT: E    9 GLN cc_start: 0.8938 (mp10) cc_final: 0.8701 (mp10)
REVERT: J   53 TYR cc_start: 0.9040 (m-80) cc_final: 0.8134 (m-80)
REVERT: J   67 ASN cc_start: 0.8744 (t0) cc_final: 0.8296 (t0)
REVERT: J   92 MET cc_start: 0.9636 (ttm) cc_final: 0.9412 (ttp)
REVERT: K    1 MET cc_start: 0.5269 (tmm) cc_final: 0.4347 (pmm)
REVERT: K    7 MET cc_start: 0.7548 (tmm) cc_final: 0.7297 (tpp)
REVERT: K   65 THR cc_start: 0.9006 (p) cc_final: 0.8791 (p)
REVERT: K   79 PHE cc_start: 0.9357 (m-80) cc_final: 0.8620 (m-10)
REVERT: L   81 ASP cc_start: 0.8101 (t70) cc_final: 0.6636 (m-30)
REVERT: N   10 LEU cc_start: 0.9156 (mp) cc_final: 0.8937 (mp)
REVERT: N   13 ASN cc_start: 0.8703 (t0) cc_final: 0.8380 (t0)
REVERT: N   20 MET cc_start: 0.9152 (ttm) cc_final: 0.8761 (tmm)
REVERT: N   21 PHE cc_start: 0.9203 (m-10) cc_final: 0.8759 (m-80)
REVERT: N  110 MET cc_start: 0.8627 (mpp) cc_final: 0.8335 (mpp)
REVERT: P   12 MET cc_start: 0.9230 (mmp) cc_final: 0.8075 (mmm)
REVERT: P   58 PHE cc_start: 0.8918 (p90) cc_final: 0.8481 (p90)
REVERT: P   84 SER cc_start: 0.8823 (m) cc_final: 0.8553 (p)
REVERT: Q   21 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9213 (pttt)
REVERT: Q   61 ILE cc_start: 0.9554 (pt) cc_final: 0.9310 (mt)
REVERT: R   15 SER cc_start: 0.9415 (t) cc_final: 0.9070 (p)
REVERT: R   70 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: R   71 LYS cc_start: 0.9016 (tmtt) cc_final: 0.8796 (tptm)
REVERT: R   85 LYS cc_start: 0.9453 (tmtt) cc_final: 0.8929 (tptp)
REVERT: S   49 LYS cc_start: 0.9383 (tptt) cc_final: 0.9148 (tptt)
REVERT: S  103 ILE cc_start: 0.9700 (pt) cc_final: 0.9427 (mp)
REVERT: U    9 GLU cc_start: 0.8043 (tt0) cc_final: 0.7812 (tt0)
REVERT: Y   29 ARG cc_start: 0.8742 (ptt-90) cc_final: 0.8040 (ptt-90)
REVERT: 0    6 LYS cc_start: 0.8969 (tttt) cc_final: 0.8180 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9426 (mmmm) cc_final: 0.8746 (mmmm)
REVERT: 0   14 MET cc_start: 0.9260 (mpp) cc_final: 0.8955 (mpp)
REVERT: 0   19 ASP cc_start: 0.8825 (m-30) cc_final: 0.8590 (m-30)
REVERT: 2   14 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8749 (mmt-90)
REVERT: Z   20 LYS cc_start: 0.9416 (tptm) cc_final: 0.8993 (tptt)
REVERT: Z   53 MET cc_start: 0.8613 (mmt) cc_final: 0.8079 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2425
  time to fit residues: 83.8667
Evaluate side-chains
  169 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 115 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 67 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 154 optimal weight:   20.0000
   chunk 231 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 41 optimal weight:   30.0000
   overall best weight:   10.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K   3 GLN
P  65 ASN
** P  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
0   5 ASN
** 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 = 0.3194 r_free = 0.3194 target = 0.043036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.030710 restraints weight = 526269.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.031648 restraints weight = 239788.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.032180 restraints weight = 156272.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.032447 restraints weight = 124423.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.032625 restraints weight = 110840.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.8130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.107  48167  Z= 0.363
  Angle     :  1.276  14.165  72350  Z= 0.511
  Chirality :  0.084   0.954   9318
  Planarity :  0.006   0.083   3647
  Dihedral  : 20.676 179.659  19449
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 35.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.61 %
    Favored  : 98.24 %
  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 are not related in a simple way.
  whole: -2.01 (0.19), residues: 1569
  helix: -0.38 (0.22), residues: 478
  sheet: -1.81 (0.28), residues: 275
  loop : -1.72 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  83 
 TYR   0.013   0.002   TYR N 112 
 PHE   0.017   0.002   PHE N  21 
 TRP   0.023   0.003   TRP P  30 
 HIS   0.008   0.002   HIS 0  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00730 /  0.36 (48167)
  covalent geometry    : angle       1.27592 /  0.51 (72350)
  hydrogen bonds       : bond        0.12372 /  6.47 ( 1693)
  hydrogen bonds       : angle       4.32422 /  1.81 ( 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
  202 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 0.994 
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: D   11 MET cc_start: 0.8187 (ppp) cc_final: 0.7959 (ppp)
REVERT: D   90 PHE cc_start: 0.8409 (m-80) cc_final: 0.8074 (m-80)
REVERT: J   53 TYR cc_start: 0.9101 (m-80) cc_final: 0.8236 (m-80)
REVERT: J   67 ASN cc_start: 0.8647 (t0) cc_final: 0.8308 (t0)
REVERT: J   92 MET cc_start: 0.9614 (ttm) cc_final: 0.9031 (tpp)
REVERT: K    1 MET cc_start: 0.5158 (tmm) cc_final: 0.4878 (pmm)
REVERT: K   65 THR cc_start: 0.9023 (p) cc_final: 0.8817 (p)
REVERT: K   79 PHE cc_start: 0.9201 (m-80) cc_final: 0.8854 (m-10)
REVERT: N   13 ASN cc_start: 0.8650 (t0) cc_final: 0.8442 (t0)
REVERT: N   20 MET cc_start: 0.9216 (ttm) cc_final: 0.8721 (tmm)
REVERT: N   21 PHE cc_start: 0.9183 (m-10) cc_final: 0.8762 (m-80)
REVERT: N  110 MET cc_start: 0.8717 (mpp) cc_final: 0.8515 (mpp)
REVERT: P   12 MET cc_start: 0.9140 (mmp) cc_final: 0.8018 (mmp)
REVERT: P   58 PHE cc_start: 0.8905 (p90) cc_final: 0.8422 (p90)
REVERT: Q   21 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9201 (pttt)
REVERT: Q   61 ILE cc_start: 0.9564 (pt) cc_final: 0.9291 (mt)
REVERT: R   26 ASP cc_start: 0.9258 (p0) cc_final: 0.9034 (p0)
REVERT: R   85 LYS cc_start: 0.9453 (tmtt) cc_final: 0.8951 (tptp)
REVERT: S   49 LYS cc_start: 0.9401 (tptt) cc_final: 0.9113 (tptt)
REVERT: S  103 ILE cc_start: 0.9723 (pt) cc_final: 0.9444 (mp)
REVERT: U    9 GLU cc_start: 0.8127 (tt0) cc_final: 0.7892 (tt0)
REVERT: Y    1 MET cc_start: 0.8360 (ppp) cc_final: 0.8149 (ppp)
REVERT: Y   30 MET cc_start: 0.8938 (mmp) cc_final: 0.8573 (mmp)
REVERT: 0    6 LYS cc_start: 0.8956 (tttt) cc_final: 0.8189 (tmtt)
REVERT: 0   11 LYS cc_start: 0.9397 (mmmm) cc_final: 0.8782 (mmmm)
REVERT: 0   14 MET cc_start: 0.9183 (mpp) cc_final: 0.8870 (mpp)
REVERT: 0   19 ASP cc_start: 0.8883 (m-30) cc_final: 0.8629 (m-30)
REVERT: 2   14 ARG cc_start: 0.8997 (mmt-90) cc_final: 0.8769 (mmt-90)
REVERT: Z   20 LYS cc_start: 0.9451 (tptm) cc_final: 0.9021 (tptt)
REVERT: Z   24 LEU cc_start: 0.9643 (pp) cc_final: 0.9392 (pp)
  outliers start: 2
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2594
  time to fit residues: 87.4025
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  : 0.825 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 127 optimal weight:   20.0000
   chunk 289 optimal weight:    4.9990
   chunk 80 optimal weight:   20.0000
   chunk 178 optimal weight:    2.9990
   chunk 174 optimal weight:    9.9990
   chunk 109 optimal weight:   20.0000
   chunk 237 optimal weight:    6.9990
   chunk 172 optimal weight:    0.8980
   chunk 234 optimal weight:   20.0000
   chunk 66 optimal weight:    9.9990
   overall best weight:    5.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K   3 GLN
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.045027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.032525 restraints weight = 509888.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.033511 restraints weight = 233063.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.034076 restraints weight = 151051.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 65)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.034395 restraints weight = 119744.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.034531 restraints weight = 106094.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.7884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  48167  Z= 0.226
  Angle     :  1.092  12.707  72350  Z= 0.439
  Chirality :  0.078   0.825   9318
  Planarity :  0.005   0.076   3647
  Dihedral  : 20.330 178.301  19449
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 24.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  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 are not related in a simple way.
  whole: -1.77 (0.20), residues: 1569
  helix: -0.13 (0.23), residues: 486
  sheet: -1.91 (0.29), residues: 265
  loop : -1.54 (0.20), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 117 
 TYR   0.013   0.002   TYR Q  31 
 PHE   0.017   0.002   PHE Q  56 
 TRP   0.014   0.002   TRP P  30 
 HIS   0.006   0.001   HIS N  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.23 (48167)
  covalent geometry    : angle       1.09229 /  0.44 (72350)
  hydrogen bonds       : bond        0.09040 /  4.74 ( 1693)
  hydrogen bonds       : angle       3.94357 /  1.66 ( 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
  207 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7919 (ppp) cc_final: 0.7717 (ppp)
REVERT: E  124 PHE cc_start: 0.7328 (t80) cc_final: 0.6998 (t80)
REVERT: E  188 MET cc_start: 0.8738 (ptm) cc_final: 0.8501 (ptm)
REVERT: J   53 TYR cc_start: 0.9096 (m-80) cc_final: 0.8226 (m-80)
REVERT: J   67 ASN cc_start: 0.8734 (t0) cc_final: 0.8274 (t0)
REVERT: J   92 MET cc_start: 0.9628 (ttm) cc_final: 0.9006 (tpp)
REVERT: J  114 LEU cc_start: 0.8311 (mp) cc_final: 0.7866 (mp)
REVERT: K    7 MET cc_start: 0.7529 (tmm) cc_final: 0.7273 (tpp)
REVERT: K   65 THR cc_start: 0.8986 (p) cc_final: 0.8778 (p)
REVERT: K   79 PHE cc_start: 0.9336 (m-80) cc_final: 0.8916 (m-10)
REVERT: N   10 LEU cc_start: 0.9133 (mp) cc_final: 0.8932 (mp)
REVERT: N   13 ASN cc_start: 0.8595 (t0) cc_final: 0.8373 (t0)
REVERT: N   20 MET cc_start: 0.9132 (ttm) cc_final: 0.8753 (tmm)
REVERT: N   21 PHE cc_start: 0.9174 (m-10) cc_final: 0.8712 (m-80)
REVERT: P   12 MET cc_start: 0.9139 (mmp) cc_final: 0.7867 (mmp)
REVERT: P   58 PHE cc_start: 0.8908 (p90) cc_final: 0.8410 (p90)
REVERT: Q   61 ILE cc_start: 0.9525 (pt) cc_final: 0.9246 (mt)
REVERT: R   85 LYS cc_start: 0.9467 (tmtt) cc_final: 0.9039 (tptp)
REVERT: R   87 GLN cc_start: 0.8982 (pp30) cc_final: 0.8249 (pp30)
REVERT: S   68 ASP cc_start: 0.8298 (p0) cc_final: 0.8045 (p0)
REVERT: S   82 MET cc_start: 0.8381 (mpp) cc_final: 0.6891 (tpt)
REVERT: S   99 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8464 (mtm180)
REVERT: S  103 ILE cc_start: 0.9702 (pt) cc_final: 0.9433 (mp)
REVERT: U    9 GLU cc_start: 0.8034 (tt0) cc_final: 0.7813 (tt0)
REVERT: Y   30 MET cc_start: 0.8860 (mmp) cc_final: 0.8512 (mmp)
REVERT: 0    6 LYS cc_start: 0.8970 (tttt) cc_final: 0.8652 (tttm)
REVERT: 0   11 LYS cc_start: 0.9389 (mmmm) cc_final: 0.8743 (mmmm)
REVERT: 0   14 MET cc_start: 0.9150 (mpp) cc_final: 0.8838 (mpp)
REVERT: 0   19 ASP cc_start: 0.8897 (m-30) cc_final: 0.8650 (m-30)
REVERT: Z   20 LYS cc_start: 0.9407 (tptm) cc_final: 0.8981 (tptt)
REVERT: Z   24 LEU cc_start: 0.9672 (pp) cc_final: 0.9464 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2620
  time to fit residues: 89.9740
Evaluate side-chains
  165 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 153 optimal weight:    3.9990
   chunk 270 optimal weight:    4.9990
   chunk 195 optimal weight:    0.7980
   chunk 78 optimal weight:   10.0000
   chunk 71 optimal weight:    9.9990
   chunk 94 optimal weight:   10.0000
   chunk 128 optimal weight:   20.0000
   chunk 197 optimal weight:    5.9990
   chunk 17 optimal weight:   20.0000
   chunk 274 optimal weight:    9.9990
   overall best weight:    5.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.045085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.032718 restraints weight = 513433.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.033675 restraints weight = 233998.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.034208 restraints weight = 151085.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 71)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.034552 restraints weight = 120515.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.034687 restraints weight = 106025.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.7936

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= 0.228
  Angle     :  1.093  12.650  72350  Z= 0.439
  Chirality :  0.077   0.830   9318
  Planarity :  0.005   0.085   3647
  Dihedral  : 20.231 177.653  19449
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 25.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    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 are not related in a simple way.
  whole: -1.68 (0.20), residues: 1569
  helix:  0.05 (0.23), residues: 486
  sheet: -1.83 (0.29), residues: 276
  loop : -1.56 (0.20), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG R  90 
 TYR   0.015   0.002   TYR Q  31 
 PHE   0.018   0.002   PHE Q  56 
 TRP   0.015   0.002   TRP R  92 
 HIS   0.008   0.001   HIS R  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00460 /  0.23 (48167)
  covalent geometry    : angle       1.09326 /  0.44 (72350)
  hydrogen bonds       : bond        0.09302 /  4.89 ( 1693)
  hydrogen bonds       : angle       3.93693 /  1.65 ( 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
  203 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.829 
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: 0.7835 (ppp) cc_final: 0.7623 (ppp)
REVERT: E  100 MET cc_start: 0.9606 (pmm) cc_final: 0.9405 (pmm)
REVERT: E  124 PHE cc_start: 0.7350 (t80) cc_final: 0.7012 (t80)
REVERT: E  188 MET cc_start: 0.8784 (ptm) cc_final: 0.8533 (ptm)
REVERT: J   53 TYR cc_start: 0.9051 (m-80) cc_final: 0.8152 (m-80)
REVERT: J   67 ASN cc_start: 0.8744 (t0) cc_final: 0.8366 (t0)
REVERT: J   92 MET cc_start: 0.9628 (ttm) cc_final: 0.9074 (tpp)
REVERT: J  114 LEU cc_start: 0.8442 (mp) cc_final: 0.8030 (mp)
REVERT: K    7 MET cc_start: 0.7568 (tmm) cc_final: 0.7324 (tpp)
REVERT: K   65 THR cc_start: 0.8976 (p) cc_final: 0.8749 (p)
REVERT: K   79 PHE cc_start: 0.9312 (m-80) cc_final: 0.8897 (m-10)
REVERT: L   81 ASP cc_start: 0.8241 (t70) cc_final: 0.6897 (m-30)
REVERT: N   10 LEU cc_start: 0.9148 (mp) cc_final: 0.8933 (mp)
REVERT: N   13 ASN cc_start: 0.8744 (t0) cc_final: 0.8388 (t0)
REVERT: N   20 MET cc_start: 0.9141 (ttm) cc_final: 0.8731 (tmm)
REVERT: N   21 PHE cc_start: 0.9176 (m-10) cc_final: 0.8714 (m-80)
REVERT: P   12 MET cc_start: 0.9140 (mmp) cc_final: 0.7957 (mmm)
REVERT: P   58 PHE cc_start: 0.8903 (p90) cc_final: 0.8393 (p90)
REVERT: P   84 SER cc_start: 0.8775 (m) cc_final: 0.8533 (p)
REVERT: Q   31 TYR cc_start: 0.8226 (t80) cc_final: 0.7809 (t80)
REVERT: Q   61 ILE cc_start: 0.9524 (pt) cc_final: 0.9262 (mt)
REVERT: R   26 ASP cc_start: 0.9238 (p0) cc_final: 0.9008 (p0)
REVERT: R   85 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9061 (tptp)
REVERT: R   87 GLN cc_start: 0.8939 (pp30) cc_final: 0.8363 (pp30)
REVERT: S   82 MET cc_start: 0.8397 (mpp) cc_final: 0.6903 (tpt)
REVERT: S   99 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8475 (mtm180)
REVERT: S  103 ILE cc_start: 0.9690 (pt) cc_final: 0.9436 (mp)
REVERT: U    9 GLU cc_start: 0.8092 (tt0) cc_final: 0.7863 (tt0)
REVERT: Y   30 MET cc_start: 0.8899 (mmp) cc_final: 0.8519 (mmp)
REVERT: 0   11 LYS cc_start: 0.9391 (mmmm) cc_final: 0.8736 (mmmm)
REVERT: 0   14 MET cc_start: 0.9149 (mpp) cc_final: 0.8832 (mpp)
REVERT: 0   19 ASP cc_start: 0.8821 (m-30) cc_final: 0.8554 (m-30)
REVERT: 2   14 ARG cc_start: 0.8605 (mmt-90) cc_final: 0.8317 (mmp80)
REVERT: Z   20 LYS cc_start: 0.9402 (tptm) cc_final: 0.8985 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2474
  time to fit residues: 84.6638
Evaluate side-chains
  163 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 201 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 107 optimal weight:   20.0000
   chunk 180 optimal weight:    1.9990
   chunk 229 optimal weight:   30.0000
   chunk 131 optimal weight:   30.0000
   chunk 181 optimal weight:    7.9990
   chunk 289 optimal weight:    7.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    6.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** 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**
Y  20 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
0   5 ASN
** 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 = 0.3231 r_free = 0.3231 target = 0.044296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.032101 restraints weight = 518095.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.032950 restraints weight = 233406.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.033497 restraints weight = 150667.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.033743 restraints weight = 119649.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.033939 restraints weight = 108141.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.8221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  48167  Z= 0.276
  Angle     :  1.147  13.089  72350  Z= 0.460
  Chirality :  0.078   0.841   9318
  Planarity :  0.005   0.074   3647
  Dihedral  : 20.326 178.126  19449
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 29.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.31 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.20), residues: 1569
  helix: -0.10 (0.23), residues: 486
  sheet: -1.91 (0.29), residues: 278
  loop : -1.64 (0.20), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Y  29 
 TYR   0.013   0.002   TYR Q  31 
 PHE   0.023   0.002   PHE Q  56 
 TRP   0.035   0.003   TRP P  30 
 HIS   0.005   0.001   HIS R  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00554 /  0.28 (48167)
  covalent geometry    : angle       1.14734 /  0.46 (72350)
  hydrogen bonds       : bond        0.10165 /  5.34 ( 1693)
  hydrogen bonds       : angle       4.05813 /  1.70 ( 3296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6367.29 seconds
wall clock time: 112 minutes 6.77 seconds (6726.77 seconds total)