Starting phenix.real_space_refine
on Mon Aug 25 11:25:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ert_28560/08_2025/8ert_28560_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ert_28560/08_2025/8ert_28560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ert_28560/08_2025/8ert_28560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ert_28560/08_2025/8ert_28560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ert_28560/08_2025/8ert_28560_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ert_28560/08_2025/8ert_28560_neut.cif"
  }
  resolution = 3.3
  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=   0.012 sd=   0.114
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 14994 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S     147      5.16       5
     C   10437      2.51       5
     N    2835      2.21       5
     O    2940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16359
  Number of models: 1
  Model: ""
    Number of chains: 21
    Chain: "A"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "B"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "C"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "D"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "F"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "G"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "J"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "K"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "L"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "M"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "N"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "O"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "Q"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "R"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "S"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "V"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "W"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "X"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 779
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
  Time building chain proxies: 3.95, per 1000 atoms: 0.24
  Number of scatterers: 16359
  At special positions: 0
  Unit cell: (94.34, 96.46, 128.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     147     16.00
     O    2940      8.00
     N    2835      7.00
     C   10437      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: 1.47
  Conformation dependent library (CDL) restraints added in 700.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3822

  Finding SS restraints...
    Secondary structure from input PDB file:
      89 helices and 0 sheets defined
      69.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 17
      removed outlier: 3.659A  pdb=" N   LEU A  17 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 31
    Processing helix  chain 'A' and resid 51 through 78
      removed outlier: 7.736A  pdb=" N   GLU A  64 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 9.430A  pdb=" N   GLU A  65 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LYS A  66 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'B' and resid 5 through 17
      removed outlier: 3.575A  pdb=" N   LYS B   9 " --> pdb=" O   SER B   5 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B  17 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 31
    Processing helix  chain 'B' and resid 51 through 78
      removed outlier: 7.576A  pdb=" N   GLU B  64 " --> pdb=" O   ASP B  60 " (cutoff:3.500A)
      removed outlier: 9.497A  pdb=" N   GLU B  65 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS B  66 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 90
    Processing helix  chain 'C' and resid 5 through 17
      removed outlier: 3.555A  pdb=" N   LYS C   9 " --> pdb=" O   SER C   5 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU C  17 " --> pdb=" O   TYR C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 31
      removed outlier: 3.569A  pdb=" N   ASP C  31 " --> pdb=" O   MET C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 78
      removed outlier: 3.577A  pdb=" N   ALA C  55 " --> pdb=" O   HIS C  51 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   GLU C  64 " --> pdb=" O   ASP C  60 " (cutoff:3.500A)
      removed outlier: 9.525A  pdb=" N   GLU C  65 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LYS C  66 " --> pdb=" O   ASN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'D' and resid 5 through 17
      removed outlier: 3.534A  pdb=" N   LYS D   9 " --> pdb=" O   SER D   5 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 31
    Processing helix  chain 'D' and resid 51 through 78
      removed outlier: 3.545A  pdb=" N   ALA D  55 " --> pdb=" O   HIS D  51 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   GLU D  64 " --> pdb=" O   ASP D  60 " (cutoff:3.500A)
      removed outlier: 9.543A  pdb=" N   GLU D  65 " --> pdb=" O   PHE D  61 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LYS D  66 " --> pdb=" O   ASN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 90
    Processing helix  chain 'E' and resid 5 through 17
      removed outlier: 3.596A  pdb=" N   LEU E  17 " --> pdb=" O   TYR E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 31
    Processing helix  chain 'E' and resid 51 through 78
      removed outlier: 3.574A  pdb=" N   ALA E  55 " --> pdb=" O   HIS E  51 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   GLU E  64 " --> pdb=" O   ASP E  60 " (cutoff:3.500A)
      removed outlier: 9.567A  pdb=" N   GLU E  65 " --> pdb=" O   PHE E  61 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LYS E  66 " --> pdb=" O   ASN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 80 through 90
    Processing helix  chain 'F' and resid 5 through 17
      removed outlier: 3.577A  pdb=" N   LEU F  17 " --> pdb=" O   TYR F  13 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 18 through 31
    Processing helix  chain 'F' and resid 51 through 63
      removed outlier: 3.708A  pdb=" N   ALA F  55 " --> pdb=" O   HIS F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 63 through 78
    Processing helix  chain 'F' and resid 80 through 90
    Processing helix  chain 'G' and resid 5 through 16
      removed outlier: 3.528A  pdb=" N   LYS G   9 " --> pdb=" O   SER G   5 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 18 through 31
    Processing helix  chain 'G' and resid 51 through 63
      removed outlier: 3.603A  pdb=" N   ALA G  55 " --> pdb=" O   HIS G  51 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 78
    Processing helix  chain 'G' and resid 80 through 90
    Processing helix  chain 'I' and resid 5 through 17
      removed outlier: 3.592A  pdb=" N   LEU I  17 " --> pdb=" O   TYR I  13 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 18 through 31
    Processing helix  chain 'I' and resid 51 through 63
    Processing helix  chain 'I' and resid 63 through 78
    Processing helix  chain 'I' and resid 80 through 90
    Processing helix  chain 'J' and resid 5 through 17
      removed outlier: 3.600A  pdb=" N   LYS J   9 " --> pdb=" O   SER J   5 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU J  17 " --> pdb=" O   TYR J  13 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 18 through 31
    Processing helix  chain 'J' and resid 51 through 78
      removed outlier: 7.588A  pdb=" N   GLU J  64 " --> pdb=" O   ASP J  60 " (cutoff:3.500A)
      removed outlier: 9.520A  pdb=" N   GLU J  65 " --> pdb=" O   PHE J  61 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS J  66 " --> pdb=" O   ASN J  62 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 80 through 90
    Processing helix  chain 'K' and resid 5 through 17
      removed outlier: 3.687A  pdb=" N   LEU K  17 " --> pdb=" O   TYR K  13 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 18 through 31
      removed outlier: 3.574A  pdb=" N   ASP K  31 " --> pdb=" O   MET K  27 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 51 through 78
      removed outlier: 3.534A  pdb=" N   ALA K  55 " --> pdb=" O   HIS K  51 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   GLU K  64 " --> pdb=" O   ASP K  60 " (cutoff:3.500A)
      removed outlier: 9.534A  pdb=" N   GLU K  65 " --> pdb=" O   PHE K  61 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   LYS K  66 " --> pdb=" O   ASN K  62 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 80 through 90
    Processing helix  chain 'L' and resid 5 through 16
    Processing helix  chain 'L' and resid 18 through 31
    Processing helix  chain 'L' and resid 51 through 78
      removed outlier: 3.840A  pdb=" N   ALA L  55 " --> pdb=" O   HIS L  51 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   GLU L  64 " --> pdb=" O   ASP L  60 " (cutoff:3.500A)
      removed outlier: 9.535A  pdb=" N   GLU L  65 " --> pdb=" O   PHE L  61 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LYS L  66 " --> pdb=" O   ASN L  62 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 90
    Processing helix  chain 'M' and resid 5 through 17
      removed outlier: 3.699A  pdb=" N   LEU M  17 " --> pdb=" O   TYR M  13 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 18 through 31
    Processing helix  chain 'M' and resid 51 through 78
      removed outlier: 3.638A  pdb=" N   ALA M  55 " --> pdb=" O   HIS M  51 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   GLU M  64 " --> pdb=" O   ASP M  60 " (cutoff:3.500A)
      removed outlier: 9.518A  pdb=" N   GLU M  65 " --> pdb=" O   PHE M  61 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LYS M  66 " --> pdb=" O   ASN M  62 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 80 through 90
    Processing helix  chain 'N' and resid 5 through 17
      removed outlier: 3.589A  pdb=" N   LEU N  17 " --> pdb=" O   TYR N  13 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 18 through 31
    Processing helix  chain 'N' and resid 51 through 78
      removed outlier: 3.739A  pdb=" N   ALA N  55 " --> pdb=" O   HIS N  51 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   GLU N  64 " --> pdb=" O   ASP N  60 " (cutoff:3.500A)
      removed outlier: 9.630A  pdb=" N   GLU N  65 " --> pdb=" O   PHE N  61 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   LYS N  66 " --> pdb=" O   ASN N  62 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 80 through 90
    Processing helix  chain 'O' and resid 5 through 17
      removed outlier: 3.545A  pdb=" N   LYS O   9 " --> pdb=" O   SER O   5 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU O  17 " --> pdb=" O   TYR O  13 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 18 through 31
    Processing helix  chain 'O' and resid 51 through 78
      removed outlier: 3.656A  pdb=" N   ALA O  55 " --> pdb=" O   HIS O  51 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   GLU O  64 " --> pdb=" O   ASP O  60 " (cutoff:3.500A)
      removed outlier: 9.482A  pdb=" N   GLU O  65 " --> pdb=" O   PHE O  61 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LYS O  66 " --> pdb=" O   ASN O  62 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 80 through 90
    Processing helix  chain 'Q' and resid 5 through 17
      removed outlier: 3.629A  pdb=" N   LEU Q  17 " --> pdb=" O   TYR Q  13 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 18 through 31
    Processing helix  chain 'Q' and resid 51 through 78
      removed outlier: 3.683A  pdb=" N   ALA Q  55 " --> pdb=" O   HIS Q  51 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   GLU Q  64 " --> pdb=" O   ASP Q  60 " (cutoff:3.500A)
      removed outlier: 9.511A  pdb=" N   GLU Q  65 " --> pdb=" O   PHE Q  61 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS Q  66 " --> pdb=" O   ASN Q  62 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 80 through 90
    Processing helix  chain 'R' and resid 5 through 17
      removed outlier: 3.586A  pdb=" N   LEU R  17 " --> pdb=" O   TYR R  13 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 18 through 31
    Processing helix  chain 'R' and resid 51 through 63
      removed outlier: 3.724A  pdb=" N   ALA R  55 " --> pdb=" O   HIS R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 63 through 78
    Processing helix  chain 'R' and resid 80 through 90
    Processing helix  chain 'S' and resid 5 through 17
      removed outlier: 3.584A  pdb=" N   LYS S   9 " --> pdb=" O   SER S   5 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU S  17 " --> pdb=" O   TYR S  13 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 18 through 31
    Processing helix  chain 'S' and resid 34 through 38
      removed outlier: 3.955A  pdb=" N   GLY S  37 " --> pdb=" O   PRO S  34 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   CYS S  38 " --> pdb=" O   GLN S  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 34 through 38'
    Processing helix  chain 'S' and resid 51 through 78
      removed outlier: 3.624A  pdb=" N   ALA S  55 " --> pdb=" O   HIS S  51 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   GLU S  64 " --> pdb=" O   ASP S  60 " (cutoff:3.500A)
      removed outlier: 9.520A  pdb=" N   GLU S  65 " --> pdb=" O   PHE S  61 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   LYS S  66 " --> pdb=" O   ASN S  62 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 80 through 90
    Processing helix  chain 'U' and resid 5 through 17
      removed outlier: 3.673A  pdb=" N   LEU U  17 " --> pdb=" O   TYR U  13 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 18 through 31
    Processing helix  chain 'U' and resid 51 through 78
      removed outlier: 7.716A  pdb=" N   GLU U  64 " --> pdb=" O   ASP U  60 " (cutoff:3.500A)
      removed outlier: 9.520A  pdb=" N   GLU U  65 " --> pdb=" O   PHE U  61 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LYS U  66 " --> pdb=" O   ASN U  62 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 80 through 90
    Processing helix  chain 'V' and resid 5 through 17
      removed outlier: 3.592A  pdb=" N   LYS V   9 " --> pdb=" O   SER V   5 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU V  17 " --> pdb=" O   TYR V  13 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 18 through 31
    Processing helix  chain 'V' and resid 51 through 78
      removed outlier: 3.515A  pdb=" N   ALA V  55 " --> pdb=" O   HIS V  51 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   GLU V  64 " --> pdb=" O   ASP V  60 " (cutoff:3.500A)
      removed outlier: 9.638A  pdb=" N   GLU V  65 " --> pdb=" O   PHE V  61 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LYS V  66 " --> pdb=" O   ASN V  62 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 80 through 90
    Processing helix  chain 'W' and resid 5 through 17
      removed outlier: 3.502A  pdb=" N   LYS W   9 " --> pdb=" O   SER W   5 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU W  17 " --> pdb=" O   TYR W  13 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 18 through 31
      removed outlier: 3.636A  pdb=" N   ASP W  31 " --> pdb=" O   MET W  27 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 51 through 78
      removed outlier: 7.737A  pdb=" N   GLU W  64 " --> pdb=" O   ASP W  60 " (cutoff:3.500A)
      removed outlier: 9.510A  pdb=" N   GLU W  65 " --> pdb=" O   PHE W  61 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LYS W  66 " --> pdb=" O   ASN W  62 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 80 through 90
    Processing helix  chain 'X' and resid 5 through 17
      removed outlier: 3.609A  pdb=" N   LYS X   9 " --> pdb=" O   SER X   5 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU X  17 " --> pdb=" O   TYR X  13 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 18 through 31
    Processing helix  chain 'X' and resid 51 through 78
      removed outlier: 3.649A  pdb=" N   ALA X  55 " --> pdb=" O   HIS X  51 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   GLU X  64 " --> pdb=" O   ASP X  60 " (cutoff:3.500A)
      removed outlier: 9.542A  pdb=" N   GLU X  65 " --> pdb=" O   PHE X  61 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS X  66 " --> pdb=" O   ASN X  62 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 80 through 90

    939 hydrogen bonds defined for protein.
    2817 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.52

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5313
        1.34 -     1.46: 3488
        1.46 -     1.58: 7684
        1.58 -     1.70: 0
        1.70 -     1.81: 252
  Bond restraints: 16737
  Sorted by residual:
  bond pdb=" CG  LYS I  88 "
       pdb=" CD  LYS I  88 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.80e+00
  bond pdb=" CE  LYS I  88 "
       pdb=" NZ  LYS I  88 "
    ideal  model  delta    sigma   weight residual
    1.489  1.446  0.043 3.00e-02 1.11e+03 2.09e+00
  bond pdb=" CG  ARG E  89 "
       pdb=" CD  ARG E  89 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CA  ILE L  39 "
       pdb=" C   ILE L  39 "
    ideal  model  delta    sigma   weight residual
    1.528  1.519  0.009 8.50e-03 1.38e+04 1.05e+00
  bond pdb=" CG  ARG L  89 "
       pdb=" CD  ARG L  89 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.02e+00
  ... (remaining 16732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 21948
        1.66 -     3.32: 451
        3.32 -     4.98: 67
        4.98 -     6.64: 18
        6.64 -     8.30: 7
  Bond angle restraints: 22491
  Sorted by residual:
  angle pdb=" CG  LYS I  88 "
        pdb=" CD  LYS I  88 "
        pdb=" CE  LYS I  88 "
      ideal   model   delta    sigma   weight residual
     111.30  103.00    8.30 2.30e+00 1.89e-01 1.30e+01
  angle pdb=" N   LYS I  88 "
        pdb=" CA  LYS I  88 "
        pdb=" CB  LYS I  88 "
      ideal   model   delta    sigma   weight residual
     110.01  114.39   -4.38 1.45e+00 4.76e-01 9.13e+00
  angle pdb=" C   ALA I  87 "
        pdb=" N   LYS I  88 "
        pdb=" CA  LYS I  88 "
      ideal   model   delta    sigma   weight residual
     120.44  116.76    3.68 1.30e+00 5.92e-01 8.00e+00
  angle pdb=" CA  TYR X  84 "
        pdb=" CB  TYR X  84 "
        pdb=" CG  TYR X  84 "
      ideal   model   delta    sigma   weight residual
     113.90  118.88   -4.98 1.80e+00 3.09e-01 7.65e+00
  angle pdb=" CB  MET I   3 "
        pdb=" CG  MET I   3 "
        pdb=" SD  MET I   3 "
      ideal   model   delta    sigma   weight residual
     112.70  120.79   -8.09 3.00e+00 1.11e-01 7.27e+00
  ... (remaining 22486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 9182
       17.75 -    35.51: 935
       35.51 -    53.26: 196
       53.26 -    71.02: 16
       71.02 -    88.77: 3
  Dihedral angle restraints: 10332
    sinusoidal: 4473
      harmonic: 5859
  Sorted by residual:
  dihedral pdb=" CA  GLU X  47 "
           pdb=" C   GLU X  47 "
           pdb=" N   LYS X  48 "
           pdb=" CA  LYS X  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.02   20.98     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  PHE O  61 "
           pdb=" C   PHE O  61 "
           pdb=" N   ASN O  62 "
           pdb=" CA  ASN O  62 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE I  61 "
           pdb=" C   PHE I  61 "
           pdb=" N   ASN I  62 "
           pdb=" CA  ASN I  62 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.40  -17.60     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 10329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1330
       0.028 -    0.056: 723
       0.056 -    0.084: 131
       0.084 -    0.111: 97
       0.111 -    0.139: 29
  Chirality restraints: 2310
  Sorted by residual:
  chirality pdb=" CA  GLU X  85 "
            pdb=" N   GLU X  85 "
            pdb=" C   GLU X  85 "
            pdb=" CB  GLU X  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  LYS I  36 "
            pdb=" N   LYS I  36 "
            pdb=" C   LYS I  36 "
            pdb=" CB  LYS I  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  GLU L  85 "
            pdb=" N   GLU L  85 "
            pdb=" C   GLU L  85 "
            pdb=" CB  GLU L  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 2307 not shown)

  Planarity restraints: 2877
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR I  84 "   -0.013 2.00e-02 2.50e+03   1.60e-02 5.14e+00
        pdb=" CG  TYR I  84 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR I  84 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR I  84 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR I  84 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR I  84 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR I  84 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR I  84 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  89 "   -0.137 9.50e-02 1.11e+02   6.17e-02 2.97e+00
        pdb=" NE  ARG L  89 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  89 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  89 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  89 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  89 "    0.133 9.50e-02 1.11e+02   6.00e-02 2.87e+00
        pdb=" NE  ARG A  89 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  89 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  89 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  89 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2874 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1810
        2.74 -     3.28: 16426
        3.28 -     3.82: 26610
        3.82 -     4.36: 31261
        4.36 -     4.90: 54350
  Nonbonded interactions: 130457
  Sorted by model distance:
  nonbonded pdb=" OG1 THR I   6 "
            pdb=" OE2 GLU I  64 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NH2 ARG M  43 "
            pdb=" OE2 GLU U  18 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" NZ  LYS I  24 "
            pdb=" OE1 GLU M  15 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OE2 GLU C  15 "
            pdb=" NE2 GLN S  45 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OE2 GLU G  30 "
            pdb=" OG1 THR G  46 "
     model   vdw
     2.273 3.040
  ... (remaining 130452 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     15.350
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
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   0.050  16737  Z= 0.136
  Angle     :  0.588   8.296  22491  Z= 0.324
  Chirality :  0.038   0.139   2310
  Planarity :  0.005   0.062   2877
  Dihedral  : 14.141  88.773   6510
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.09 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.06 %
    Favored  : 99.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.18), residues: 1953
  helix:  0.79 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.37 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG Q  89 
 TYR   0.039   0.002   TYR I  84 
 PHE   0.009   0.001   PHE C  61 
 TRP   0.013   0.001   TRP X  68 
 HIS   0.011   0.001   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (16737)
  covalent geometry    : angle       0.58779 (22491)
  hydrogen bonds       : bond        0.11054 (  939)
  hydrogen bonds       : angle       5.60570 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  564 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 564
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7218 (tpt) cc_final: 0.6898 (tmm)
REVERT: A   16 ASP cc_start: 0.8159 (t0) cc_final: 0.7901 (t70)
REVERT: A   31 ASP cc_start: 0.8139 (m-30) cc_final: 0.7910 (m-30)
REVERT: C    1 MET cc_start: 0.6679 (ttp) cc_final: 0.6355 (ttp)
REVERT: E    1 MET cc_start: 0.6697 (tmm) cc_final: 0.6243 (ppp)
REVERT: G   15 GLU cc_start: 0.7463 (tt0) cc_final: 0.7178 (tt0)
REVERT: K   70 MET cc_start: 0.8468 (mtp) cc_final: 0.8258 (mtm)
REVERT: M    1 MET cc_start: 0.6300 (tmm) cc_final: 0.5964 (ppp)
REVERT: N   46 THR cc_start: 0.8276 (p) cc_final: 0.8035 (p)
REVERT: S    9 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8205 (mttp)
REVERT: S   45 GLN cc_start: 0.8394 (mp10) cc_final: 0.8191 (mp10)
REVERT: S   66 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7983 (mmtp)
REVERT: U    1 MET cc_start: 0.7259 (tpp) cc_final: 0.6985 (tmm)
REVERT: U   58 MET cc_start: 0.8720 (mtp) cc_final: 0.8457 (ttm)
REVERT: V   70 MET cc_start: 0.8195 (mtp) cc_final: 0.7555 (mtp)
REVERT: X   27 MET cc_start: 0.9014 (ttp) cc_final: 0.8414 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 564
  average time/residue: 0.1857
  time to fit residues: 142.6787
Evaluate side-chains
  537 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 537
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
N  51 HIS
Q  62 ASN
** U  51 HIS ** 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 = 0.3737 r_free = 0.3737 target = 0.146235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.117759 restraints weight = 20168.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.35
r_work: 0.3251 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  16737  Z= 0.139
  Angle     :  0.574   8.073  22491  Z= 0.305
  Chirality :  0.040   0.165   2310
  Planarity :  0.005   0.045   2877
  Dihedral  :  3.868  18.769   2163
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.70 %
    Favored  : 91.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.18), residues: 1953
  helix:  1.11 (0.13), residues: 1365
  sheet:  None (None), residues: 0
  loop : -1.51 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Q  89 
 TYR   0.023   0.002   TYR I  84 
 PHE   0.009   0.001   PHE N  25 
 TRP   0.008   0.001   TRP V  94 
 HIS   0.013   0.001   HIS N  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (16737)
  covalent geometry    : angle       0.57383 (22491)
  hydrogen bonds       : bond        0.04253 (  939)
  hydrogen bonds       : angle       4.60015 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  561 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 548
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7740 (tpt) cc_final: 0.7029 (tmm)
REVERT: A   31 ASP cc_start: 0.8638 (m-30) cc_final: 0.8165 (m-30)
REVERT: A   64 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: C    1 MET cc_start: 0.6717 (ttp) cc_final: 0.6388 (ttp)
REVERT: C   30 GLU cc_start: 0.7506 (mp0) cc_final: 0.7009 (mp0)
REVERT: D    1 MET cc_start: 0.8270 (tmm) cc_final: 0.7759 (tpp)
REVERT: D   15 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8536 (mm-30)
REVERT: D   45 GLN cc_start: 0.8798 (mt0) cc_final: 0.8578 (mt0)
REVERT: E    1 MET cc_start: 0.7191 (tmm) cc_final: 0.6567 (ppp)
REVERT: E   13 TYR cc_start: 0.8622 (m-10) cc_final: 0.8169 (m-80)
REVERT: F   15 GLU cc_start: 0.8175 (tt0) cc_final: 0.7909 (tt0)
REVERT: G   45 GLN cc_start: 0.8860 (mp10) cc_final: 0.8509 (mp10)
REVERT: I   62 ASN cc_start: 0.8780 (m110) cc_final: 0.8454 (m110)
REVERT: J   31 ASP cc_start: 0.8493 (m-30) cc_final: 0.8261 (m-30)
REVERT: J   32 TYR cc_start: 0.8891 (t80) cc_final: 0.8665 (t80)
REVERT: K    9 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8408 (mttm)
REVERT: K   30 GLU cc_start: 0.7598 (mp0) cc_final: 0.7293 (mp0)
REVERT: L   15 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7973 (mm-30)
REVERT: M    1 MET cc_start: 0.6840 (tmm) cc_final: 0.6315 (ppp)
REVERT: M   13 TYR cc_start: 0.8718 (m-10) cc_final: 0.8364 (m-80)
REVERT: N    1 MET cc_start: 0.7353 (tmm) cc_final: 0.6704 (tpp)
REVERT: O   62 ASN cc_start: 0.8816 (m-40) cc_final: 0.8378 (m110)
REVERT: O   64 GLU cc_start: 0.8188 (mp0) cc_final: 0.7813 (mt-10)
REVERT: O   79 ASN cc_start: 0.7878 (m-40) cc_final: 0.7528 (m110)
REVERT: R    1 MET cc_start: 0.7073 (tmm) cc_final: 0.6362 (tpp)
REVERT: R   66 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8144 (mttm)
REVERT: S   45 GLN cc_start: 0.8881 (mp10) cc_final: 0.8583 (mp10)
REVERT: U    1 MET cc_start: 0.7723 (tpp) cc_final: 0.7086 (tmm)
REVERT: U   58 MET cc_start: 0.8879 (mtp) cc_final: 0.8630 (ttm)
REVERT: W   30 GLU cc_start: 0.7577 (mp0) cc_final: 0.7087 (mp0)
REVERT: X   15 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8470 (mm-30)
REVERT: X   27 MET cc_start: 0.8852 (ttp) cc_final: 0.8427 (ttm)
  outliers start: 13
  outliers final: 6
  residues processed: 549
  average time/residue: 0.1786
  time to fit residues: 133.7654
Evaluate side-chains
  539 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 533
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain G residue   16 ASP
Chi-restraints excluded: chain I residue   64 GLU
Chi-restraints excluded: chain N residue   85 GLU
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 139 optimal weight:    8.9990
   chunk 180 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9980
   chunk 188 optimal weight:    6.9990
   chunk 164 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 165 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C  62 ASN
** F  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  62 ASN
U  45 GLN
** U  51 HIS ** 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 = 0.3719 r_free = 0.3719 target = 0.144747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.116185 restraints weight = 20381.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.35
r_work: 0.3236 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16737  Z= 0.127
  Angle     :  0.560   7.975  22491  Z= 0.299
  Chirality :  0.039   0.179   2310
  Planarity :  0.004   0.040   2877
  Dihedral  :  3.807  16.974   2163
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.70 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.18), residues: 1953
  helix:  1.19 (0.13), residues: 1365
  sheet:  None (None), residues: 0
  loop : -1.42 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Q  89 
 TYR   0.018   0.001   TYR I  84 
 PHE   0.008   0.001   PHE N  25 
 TRP   0.006   0.001   TRP I  94 
 HIS   0.015   0.001   HIS F  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (16737)
  covalent geometry    : angle       0.55971 (22491)
  hydrogen bonds       : bond        0.03999 (  939)
  hydrogen bonds       : angle       4.52110 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  563 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 546
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7685 (tpt) cc_final: 0.6988 (tmm)
REVERT: A   31 ASP cc_start: 0.8715 (m-30) cc_final: 0.8166 (m-30)
REVERT: A   64 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7466 (mm-30)
REVERT: C   30 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7152 (mp0)
REVERT: D    1 MET cc_start: 0.8290 (tmm) cc_final: 0.7774 (tpp)
REVERT: D   15 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8420 (mm-30)
REVERT: D   31 ASP cc_start: 0.7973 (t0) cc_final: 0.7762 (t70)
REVERT: D   45 GLN cc_start: 0.8754 (mt0) cc_final: 0.8513 (mt0)
REVERT: D   62 ASN cc_start: 0.8711 (m110) cc_final: 0.8442 (m110)
REVERT: D   86 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7863 (mmtm)
REVERT: E    1 MET cc_start: 0.7300 (tmm) cc_final: 0.6702 (ppp)
REVERT: E   13 TYR cc_start: 0.8725 (m-10) cc_final: 0.8117 (m-80)
REVERT: F   62 ASN cc_start: 0.8931 (m110) cc_final: 0.8582 (m110)
REVERT: G   45 GLN cc_start: 0.8926 (mp10) cc_final: 0.8559 (mp10)
REVERT: G   62 ASN cc_start: 0.9003 (m110) cc_final: 0.8686 (m110)
REVERT: I   62 ASN cc_start: 0.8784 (m110) cc_final: 0.8414 (m-40)
REVERT: J   32 TYR cc_start: 0.8883 (t80) cc_final: 0.8652 (t80)
REVERT: K    1 MET cc_start: 0.6661 (tmm) cc_final: 0.5335 (pmm)
REVERT: K    3 MET cc_start: 0.6737 (ptm) cc_final: 0.6533 (ppp)
REVERT: K   30 GLU cc_start: 0.7535 (mp0) cc_final: 0.7288 (mp0)
REVERT: M    1 MET cc_start: 0.6938 (tmm) cc_final: 0.6432 (ppp)
REVERT: M    3 MET cc_start: 0.6079 (tmm) cc_final: 0.5854 (tmm)
REVERT: M   13 TYR cc_start: 0.8777 (m-10) cc_final: 0.8231 (m-80)
REVERT: O   65 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8193 (mm-30)
REVERT: O   79 ASN cc_start: 0.7745 (m-40) cc_final: 0.7468 (m110)
REVERT: R   66 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8212 (mttm)
REVERT: S   62 ASN cc_start: 0.8942 (m110) cc_final: 0.8306 (m110)
REVERT: S   64 GLU cc_start: 0.8190 (mp0) cc_final: 0.7890 (mt-10)
REVERT: U    1 MET cc_start: 0.7789 (tpp) cc_final: 0.7112 (tmm)
REVERT: U   58 MET cc_start: 0.8848 (mtp) cc_final: 0.8594 (ttm)
REVERT: W   30 GLU cc_start: 0.7553 (mp0) cc_final: 0.6929 (mp0)
REVERT: X   15 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8225 (mm-30)
REVERT: X   27 MET cc_start: 0.8844 (ttp) cc_final: 0.8485 (ttm)
  outliers start: 17
  outliers final: 12
  residues processed: 548
  average time/residue: 0.1864
  time to fit residues: 139.1944
Evaluate side-chains
  543 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 531
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain I residue   64 GLU
Chi-restraints excluded: chain N residue   85 GLU
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain O residue   43 ARG
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain S residue   88 LYS
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Chi-restraints excluded: chain X residue   16 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 151 optimal weight:    0.8980
   chunk 177 optimal weight:    1.9990
   chunk 181 optimal weight:    7.9990
   chunk 156 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 136 optimal weight:    5.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
F  62 ASN
G  62 ASN
J  62 ASN
N  51 HIS
O  62 ASN
Q  62 ASN
U  51 HIS
** V  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
V  62 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.155595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126142 restraints weight = 19797.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.29
r_work: 0.3404 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  16737  Z= 0.199
  Angle     :  0.607   9.102  22491  Z= 0.321
  Chirality :  0.042   0.193   2310
  Planarity :  0.004   0.037   2877
  Dihedral  :  3.871  17.020   2163
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.29 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.18), residues: 1953
  helix:  1.05 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.14 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Q  89 
 TYR   0.016   0.002   TYR C  32 
 PHE   0.009   0.001   PHE K  25 
 TRP   0.010   0.001   TRP V  94 
 HIS   0.015   0.002   HIS L  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (16737)
  covalent geometry    : angle       0.60667 (22491)
  hydrogen bonds       : bond        0.04651 (  939)
  hydrogen bonds       : angle       4.57415 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  563 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 543
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7585 (tpt) cc_final: 0.6956 (tmm)
REVERT: C   30 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7217 (mp0)
REVERT: D    1 MET cc_start: 0.8132 (tmm) cc_final: 0.7609 (tpp)
REVERT: D   15 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8370 (mm-30)
REVERT: D   31 ASP cc_start: 0.8269 (t0) cc_final: 0.7977 (t70)
REVERT: D   86 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8090 (mmtm)
REVERT: E    1 MET cc_start: 0.7350 (tmm) cc_final: 0.6639 (ppp)
REVERT: E    3 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5609 (tmm)
REVERT: E   45 GLN cc_start: 0.8400 (mt0) cc_final: 0.8169 (mt0)
REVERT: F   62 ASN cc_start: 0.8993 (m-40) cc_final: 0.8697 (m110)
REVERT: G   45 GLN cc_start: 0.8949 (mp10) cc_final: 0.8741 (mp10)
REVERT: G   62 ASN cc_start: 0.9049 (m-40) cc_final: 0.8826 (m-40)
REVERT: G   65 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7772 (mm-30)
REVERT: I   62 ASN cc_start: 0.8935 (m110) cc_final: 0.8685 (m110)
REVERT: K    1 MET cc_start: 0.6731 (tmm) cc_final: 0.5444 (pmm)
REVERT: L    8 CYS cc_start: 0.8518 (m) cc_final: 0.8244 (m)
REVERT: L   13 TYR cc_start: 0.8667 (m-80) cc_final: 0.8414 (m-80)
REVERT: M   13 TYR cc_start: 0.8719 (m-10) cc_final: 0.8444 (m-10)
REVERT: M   62 ASN cc_start: 0.8996 (m-40) cc_final: 0.8414 (m110)
REVERT: N    1 MET cc_start: 0.7293 (tmm) cc_final: 0.6767 (mtp)
REVERT: O   62 ASN cc_start: 0.8847 (m-40) cc_final: 0.8554 (m110)
REVERT: O   64 GLU cc_start: 0.7989 (mp0) cc_final: 0.7764 (mt-10)
REVERT: O   79 ASN cc_start: 0.7958 (m-40) cc_final: 0.7683 (m110)
REVERT: R    1 MET cc_start: 0.7130 (tmm) cc_final: 0.6353 (tpp)
REVERT: U    1 MET cc_start: 0.7705 (tpp) cc_final: 0.7060 (tmm)
REVERT: U   58 MET cc_start: 0.8800 (mtp) cc_final: 0.8575 (ttm)
REVERT: W   30 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7085 (mp0)
REVERT: X   27 MET cc_start: 0.8974 (ttp) cc_final: 0.8602 (ttm)
REVERT: X   51 HIS cc_start: 0.7520 (p90) cc_final: 0.7310 (p-80)
REVERT: X   66 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7503 (mmmt)
  outliers start: 20
  outliers final: 16
  residues processed: 544
  average time/residue: 0.1802
  time to fit residues: 133.2593
Evaluate side-chains
  548 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 531
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain E residue    3 MET
Chi-restraints excluded: chain I residue   57 LEU
Chi-restraints excluded: chain I residue   64 GLU
Chi-restraints excluded: chain L residue   16 ASP
Chi-restraints excluded: chain N residue   85 GLU
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain O residue   43 ARG
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain S residue   88 LYS
Chi-restraints excluded: chain U residue   27 MET
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Chi-restraints excluded: chain X residue   16 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 154 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   chunk 142 optimal weight:    0.9980
   chunk 168 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 186 optimal weight:    0.8980
   chunk 176 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 131 optimal weight:    0.2980
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** N  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  62 ASN
U  45 GLN
** V  51 HIS ** 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 = 0.3930 r_free = 0.3930 target = 0.159318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131241 restraints weight = 19678.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.19
r_work: 0.3476 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16737  Z= 0.124
  Angle     :  0.575   8.739  22491  Z= 0.307
  Chirality :  0.039   0.201   2310
  Planarity :  0.004   0.037   2877
  Dihedral  :  3.793  16.913   2163
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 14.70 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.18), residues: 1953
  helix:  1.10 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.13 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E  89 
 TYR   0.014   0.001   TYR X  84 
 PHE   0.008   0.001   PHE N  25 
 TRP   0.009   0.001   TRP F  94 
 HIS   0.012   0.001   HIS R  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (16737)
  covalent geometry    : angle       0.57532 (22491)
  hydrogen bonds       : bond        0.03837 (  939)
  hydrogen bonds       : angle       4.46242 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  564 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 549
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7430 (tpt) cc_final: 0.7030 (tmm)
REVERT: D    1 MET cc_start: 0.8014 (tmm) cc_final: 0.7540 (tpp)
REVERT: D   15 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8336 (mm-30)
REVERT: D   16 ASP cc_start: 0.8522 (t70) cc_final: 0.8118 (t0)
REVERT: D   86 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8150 (mmtm)
REVERT: E    1 MET cc_start: 0.7347 (tmm) cc_final: 0.6667 (ppp)
REVERT: E    3 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5598 (tmm)
REVERT: F   62 ASN cc_start: 0.8829 (m-40) cc_final: 0.8565 (m110)
REVERT: G   45 GLN cc_start: 0.8869 (mp10) cc_final: 0.8572 (mp10)
REVERT: G   62 ASN cc_start: 0.8999 (m-40) cc_final: 0.8738 (m110)
REVERT: I   62 ASN cc_start: 0.8803 (m110) cc_final: 0.8552 (m110)
REVERT: K    1 MET cc_start: 0.6773 (tmm) cc_final: 0.5524 (pmm)
REVERT: K    3 MET cc_start: 0.6843 (ppp) cc_final: 0.6623 (ppp)
REVERT: K    9 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8451 (mttm)
REVERT: L    8 CYS cc_start: 0.8380 (m) cc_final: 0.8131 (m)
REVERT: L   13 TYR cc_start: 0.8615 (m-80) cc_final: 0.8364 (m-80)
REVERT: M   13 TYR cc_start: 0.8623 (m-10) cc_final: 0.8219 (m-10)
REVERT: M   62 ASN cc_start: 0.8850 (m-40) cc_final: 0.8389 (m110)
REVERT: O   62 ASN cc_start: 0.8799 (m-40) cc_final: 0.8461 (m110)
REVERT: O   64 GLU cc_start: 0.7869 (mp0) cc_final: 0.7616 (mt-10)
REVERT: O   79 ASN cc_start: 0.7595 (m-40) cc_final: 0.7377 (m110)
REVERT: Q   31 ASP cc_start: 0.8280 (m-30) cc_final: 0.8077 (m-30)
REVERT: R   66 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8287 (mttm)
REVERT: U    1 MET cc_start: 0.7600 (tpp) cc_final: 0.6806 (ppp)
REVERT: U   58 MET cc_start: 0.8664 (mtp) cc_final: 0.8427 (ttm)
REVERT: W   30 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7162 (mp0)
REVERT: X   15 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8200 (mm-30)
REVERT: X   27 MET cc_start: 0.8934 (ttp) cc_final: 0.8585 (ttm)
REVERT: X   51 HIS cc_start: 0.7310 (p90) cc_final: 0.6999 (p90)
REVERT: X   66 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7458 (mmmt)
  outliers start: 15
  outliers final: 10
  residues processed: 550
  average time/residue: 0.1632
  time to fit residues: 122.3486
Evaluate side-chains
  545 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 534
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 MET
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain E residue    3 MET
Chi-restraints excluded: chain L residue   16 ASP
Chi-restraints excluded: chain N residue   85 GLU
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain O residue   43 ARG
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Chi-restraints excluded: chain X residue   16 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 159 optimal weight:    5.9990
   chunk 158 optimal weight:    0.8980
   chunk 186 optimal weight:    9.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 105 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
E  62 ASN
F  51 HIS
G  79 ASN
N  51 HIS
N  62 ASN
Q  62 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.149483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121568 restraints weight = 19883.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.15
r_work: 0.3304 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  16737  Z= 0.287
  Angle     :  0.678   9.876  22491  Z= 0.358
  Chirality :  0.044   0.218   2310
  Planarity :  0.005   0.042   2877
  Dihedral  :  4.078  18.248   2163
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.81 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.18), residues: 1953
  helix:  0.86 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.17 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  43 
 TYR   0.018   0.002   TYR C  32 
 PHE   0.010   0.001   PHE N  25 
 TRP   0.010   0.001   TRP I  94 
 HIS   0.014   0.002   HIS F  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 (16737)
  covalent geometry    : angle       0.67790 (22491)
  hydrogen bonds       : bond        0.05355 (  939)
  hydrogen bonds       : angle       4.75480 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  586 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 558
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7474 (tpt) cc_final: 0.6841 (tmm)
REVERT: D    1 MET cc_start: 0.8072 (tmm) cc_final: 0.7461 (tpp)
REVERT: D   15 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8346 (mm-30)
REVERT: D   16 ASP cc_start: 0.8790 (t70) cc_final: 0.8403 (t0)
REVERT: D   66 LYS cc_start: 0.8240 (mmtm) cc_final: 0.8025 (mmmt)
REVERT: D   70 MET cc_start: 0.8828 (mtp) cc_final: 0.8472 (mtp)
REVERT: D   86 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8168 (mmtm)
REVERT: E    3 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5499 (tmm)
REVERT: G   24 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8790 (mtmm)
REVERT: G   45 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8599 (mp10)
REVERT: G   62 ASN cc_start: 0.9072 (m-40) cc_final: 0.8849 (m-40)
REVERT: I   62 ASN cc_start: 0.8904 (m110) cc_final: 0.8670 (m110)
REVERT: K    1 MET cc_start: 0.6768 (tmm) cc_final: 0.5587 (pmm)
REVERT: K    3 MET cc_start: 0.6883 (ppp) cc_final: 0.6197 (ppp)
REVERT: L    8 CYS cc_start: 0.8799 (m) cc_final: 0.8572 (m)
REVERT: M   62 ASN cc_start: 0.8965 (m-40) cc_final: 0.8440 (m110)
REVERT: N   60 ASP cc_start: 0.7970 (t0) cc_final: 0.7720 (t0)
REVERT: O   62 ASN cc_start: 0.8879 (m-40) cc_final: 0.8631 (m110)
REVERT: O   64 GLU cc_start: 0.8159 (mp0) cc_final: 0.7860 (mt-10)
REVERT: O   79 ASN cc_start: 0.8002 (m-40) cc_final: 0.7790 (m110)
REVERT: Q   45 GLN cc_start: 0.8253 (mt0) cc_final: 0.7978 (mt0)
REVERT: R    1 MET cc_start: 0.7353 (tmm) cc_final: 0.6492 (tpp)
REVERT: U    1 MET cc_start: 0.7921 (tpp) cc_final: 0.6804 (ppp)
REVERT: U   58 MET cc_start: 0.8867 (mtp) cc_final: 0.8480 (mtp)
REVERT: W   30 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7398 (mp0)
REVERT: X   27 MET cc_start: 0.8963 (ttp) cc_final: 0.8609 (ttm)
REVERT: X   60 ASP cc_start: 0.7885 (t0) cc_final: 0.7595 (t0)
REVERT: X   66 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7710 (mmmt)
  outliers start: 28
  outliers final: 18
  residues processed: 561
  average time/residue: 0.1420
  time to fit residues: 109.1117
Evaluate side-chains
  564 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 544
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   27 MET
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain E residue    3 MET
Chi-restraints excluded: chain G residue   45 GLN
Chi-restraints excluded: chain I residue   57 LEU
Chi-restraints excluded: chain L residue   16 ASP
Chi-restraints excluded: chain M residue   88 LYS
Chi-restraints excluded: chain N residue   85 GLU
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain S residue   88 LYS
Chi-restraints excluded: chain U residue   27 MET
Chi-restraints excluded: chain U residue   85 GLU
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Chi-restraints excluded: chain X residue   16 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 158 optimal weight:    0.9990
   chunk 145 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    0.2980
   chunk 49 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
F  62 ASN
** N  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  62 ASN
** V  51 HIS ** 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 = 0.3910 r_free = 0.3910 target = 0.158175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128749 restraints weight = 19713.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.31
r_work: 0.3428 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16737  Z= 0.133
  Angle     :  0.613   9.577  22491  Z= 0.326
  Chirality :  0.039   0.227   2310
  Planarity :  0.005   0.050   2877
  Dihedral  :  3.918  16.712   2163
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.75 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.18), residues: 1953
  helix:  0.99 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.16 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG Q  89 
 TYR   0.011   0.001   TYR E  84 
 PHE   0.008   0.001   PHE N  25 
 TRP   0.007   0.001   TRP U  68 
 HIS   0.013   0.001   HIS R  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (16737)
  covalent geometry    : angle       0.61326 (22491)
  hydrogen bonds       : bond        0.04031 (  939)
  hydrogen bonds       : angle       4.51759 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  566 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 545
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7461 (tpt) cc_final: 0.6952 (tmm)
REVERT: D    1 MET cc_start: 0.8079 (tmm) cc_final: 0.7562 (tpp)
REVERT: D   15 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8158 (mm-30)
REVERT: D   16 ASP cc_start: 0.8550 (t70) cc_final: 0.8142 (t0)
REVERT: D   43 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8297 (tpp-160)
REVERT: E    3 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5627 (tmm)
REVERT: G   45 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8523 (mp10)
REVERT: G   65 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7768 (mm-30)
REVERT: K    1 MET cc_start: 0.6794 (tmm) cc_final: 0.5665 (pmm)
REVERT: K    3 MET cc_start: 0.6794 (ppp) cc_final: 0.6071 (ppp)
REVERT: K   79 ASN cc_start: 0.8092 (m110) cc_final: 0.7743 (m110)
REVERT: L    8 CYS cc_start: 0.8449 (m) cc_final: 0.8224 (m)
REVERT: M   13 TYR cc_start: 0.8768 (m-10) cc_final: 0.8534 (m-10)
REVERT: M   62 ASN cc_start: 0.8801 (m-40) cc_final: 0.8302 (m110)
REVERT: N   66 LYS cc_start: 0.8368 (mmtp) cc_final: 0.7938 (mttp)
REVERT: O   62 ASN cc_start: 0.8664 (m-40) cc_final: 0.8379 (m110)
REVERT: O   64 GLU cc_start: 0.7988 (mp0) cc_final: 0.7715 (mt-10)
REVERT: Q   31 ASP cc_start: 0.8342 (m-30) cc_final: 0.8116 (m-30)
REVERT: R   66 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8218 (mttm)
REVERT: U    1 MET cc_start: 0.7816 (tpp) cc_final: 0.6838 (ppp)
REVERT: U   58 MET cc_start: 0.8720 (mtp) cc_final: 0.8376 (ttm)
REVERT: U   64 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7305 (mm-30)
REVERT: W   30 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6978 (mp0)
REVERT: X   27 MET cc_start: 0.8933 (ttp) cc_final: 0.8609 (ttm)
REVERT: X   66 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7396 (mmmt)
  outliers start: 21
  outliers final: 14
  residues processed: 547
  average time/residue: 0.1502
  time to fit residues: 112.8992
Evaluate side-chains
  553 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 537
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 MET
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain E residue    3 MET
Chi-restraints excluded: chain G residue   45 GLN
Chi-restraints excluded: chain G residue   57 LEU
Chi-restraints excluded: chain J residue   27 MET
Chi-restraints excluded: chain L residue   16 ASP
Chi-restraints excluded: chain M residue   88 LYS
Chi-restraints excluded: chain N residue   85 GLU
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain O residue   43 ARG
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain U residue   57 LEU
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Chi-restraints excluded: chain X residue   16 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0980
   chunk 103 optimal weight:    0.0070
   chunk 144 optimal weight:    9.9990
   chunk 148 optimal weight:    0.0070
   chunk 66 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 138 optimal weight:    0.0000
   chunk 4 optimal weight:    0.0980
   chunk 100 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.0420

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

Flipped N/Q/H residues before XYZ refinement:
F  51 HIS
G  62 ASN
I  62 ASN
** L  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  79 ASN
** V  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.162254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.133107 restraints weight = 19675.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.30
r_work: 0.3468 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16737  Z= 0.124
  Angle     :  0.615  10.030  22491  Z= 0.325
  Chirality :  0.039   0.238   2310
  Planarity :  0.005   0.051   2877
  Dihedral  :  3.806  16.607   2163
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 17.28 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.18), residues: 1953
  helix:  1.11 (0.13), residues: 1365
  sheet:  None (None), residues: 0
  loop : -1.39 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG F  43 
 TYR   0.012   0.001   TYR X  84 
 PHE   0.008   0.001   PHE N  25 
 TRP   0.005   0.001   TRP I  68 
 HIS   0.016   0.001   HIS L  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (16737)
  covalent geometry    : angle       0.61454 (22491)
  hydrogen bonds       : bond        0.03549 (  939)
  hydrogen bonds       : angle       4.47438 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  561 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 545
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7526 (tpt) cc_final: 0.7096 (tmm)
REVERT: C   30 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7061 (mp0)
REVERT: D    1 MET cc_start: 0.8044 (tmm) cc_final: 0.7589 (tpp)
REVERT: D   15 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8169 (mm-30)
REVERT: D   16 ASP cc_start: 0.8475 (t70) cc_final: 0.8090 (t0)
REVERT: E    3 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5594 (tmm)
REVERT: F    1 MET cc_start: 0.7205 (tmm) cc_final: 0.6564 (mtm)
REVERT: G   43 ARG cc_start: 0.8712 (mtp180) cc_final: 0.8497 (mtp180)
REVERT: G   79 ASN cc_start: 0.7372 (m-40) cc_final: 0.7089 (m110)
REVERT: I    1 MET cc_start: 0.8014 (tpt) cc_final: 0.7753 (tpp)
REVERT: K    1 MET cc_start: 0.6889 (tmm) cc_final: 0.5799 (pmm)
REVERT: K    3 MET cc_start: 0.6930 (ppp) cc_final: 0.6176 (ppp)
REVERT: K   47 GLU cc_start: 0.8306 (tp30) cc_final: 0.8093 (mm-30)
REVERT: L   23 LYS cc_start: 0.8765 (mttm) cc_final: 0.8416 (ttpt)
REVERT: L   62 ASN cc_start: 0.8693 (m-40) cc_final: 0.8493 (m-40)
REVERT: M    3 MET cc_start: 0.6096 (tmm) cc_final: 0.5791 (tmm)
REVERT: M   13 TYR cc_start: 0.8707 (m-10) cc_final: 0.8244 (m-10)
REVERT: N   46 THR cc_start: 0.8544 (p) cc_final: 0.8299 (p)
REVERT: O   62 ASN cc_start: 0.8527 (m-40) cc_final: 0.8256 (m-40)
REVERT: O   64 GLU cc_start: 0.8107 (mp0) cc_final: 0.7725 (mt-10)
REVERT: O   65 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7986 (mm-30)
REVERT: R    1 MET cc_start: 0.7157 (tmm) cc_final: 0.6768 (tmm)
REVERT: R   66 LYS cc_start: 0.8315 (mmtp) cc_final: 0.7875 (mttm)
REVERT: U    1 MET cc_start: 0.7833 (tpp) cc_final: 0.6945 (ppp)
REVERT: U   58 MET cc_start: 0.8717 (mtp) cc_final: 0.8501 (ttm)
REVERT: W   30 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6978 (mp0)
REVERT: X   27 MET cc_start: 0.8826 (ttp) cc_final: 0.8506 (ttm)
REVERT: X   43 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8547 (tpp80)
  outliers start: 16
  outliers final: 10
  residues processed: 548
  average time/residue: 0.1569
  time to fit residues: 118.6810
Evaluate side-chains
  544 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 533
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 MET
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain E residue    3 MET
Chi-restraints excluded: chain G residue   57 LEU
Chi-restraints excluded: chain L residue   16 ASP
Chi-restraints excluded: chain M residue   88 LYS
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain O residue   43 ARG
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 138 optimal weight:   10.0000
   chunk 172 optimal weight:    0.9990
   chunk 126 optimal weight:   10.0000
   chunk 170 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 111 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 160 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** L  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 ASN
** N  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  62 ASN
** V  51 HIS ** 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 = 0.3931 r_free = 0.3931 target = 0.159379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.131529 restraints weight = 19612.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.17
r_work: 0.3464 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16737  Z= 0.135
  Angle     :  0.643   9.456  22491  Z= 0.339
  Chirality :  0.041   0.248   2310
  Planarity :  0.005   0.057   2877
  Dihedral  :  3.796  16.021   2163
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 17.99 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.18), residues: 1953
  helix:  1.04 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.12 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG O  89 
 TYR   0.016   0.001   TYR K  32 
 PHE   0.008   0.001   PHE N  25 
 TRP   0.010   0.001   TRP S  94 
 HIS   0.014   0.001   HIS R  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (16737)
  covalent geometry    : angle       0.64329 (22491)
  hydrogen bonds       : bond        0.03823 (  939)
  hydrogen bonds       : angle       4.49754 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  551 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 535
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7620 (tpt) cc_final: 0.7136 (tmm)
REVERT: C   30 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7235 (mp0)
REVERT: D    1 MET cc_start: 0.8021 (tmm) cc_final: 0.7533 (tpp)
REVERT: D   16 ASP cc_start: 0.8545 (t70) cc_final: 0.8194 (t0)
REVERT: E    3 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.5520 (tmm)
REVERT: G   43 ARG cc_start: 0.8848 (mtp180) cc_final: 0.8595 (mtp180)
REVERT: G   65 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8143 (mm-30)
REVERT: I    1 MET cc_start: 0.8003 (tpt) cc_final: 0.7644 (tpp)
REVERT: K    1 MET cc_start: 0.6794 (tmm) cc_final: 0.5834 (pmm)
REVERT: K    3 MET cc_start: 0.6969 (ppp) cc_final: 0.6162 (ppp)
REVERT: L   23 LYS cc_start: 0.8833 (mttm) cc_final: 0.8508 (ttpt)
REVERT: M    3 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5583 (tmm)
REVERT: M   13 TYR cc_start: 0.8888 (m-10) cc_final: 0.8369 (m-10)
REVERT: M   62 ASN cc_start: 0.8559 (m-40) cc_final: 0.8300 (m-40)
REVERT: O   62 ASN cc_start: 0.8698 (m-40) cc_final: 0.8353 (m110)
REVERT: O   64 GLU cc_start: 0.8302 (mp0) cc_final: 0.8014 (mt-10)
REVERT: O   89 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7842 (mtm110)
REVERT: R    1 MET cc_start: 0.7321 (tmm) cc_final: 0.6886 (tmm)
REVERT: R   66 LYS cc_start: 0.8635 (mmtp) cc_final: 0.8336 (mttm)
REVERT: S   64 GLU cc_start: 0.8301 (mp0) cc_final: 0.8064 (mt-10)
REVERT: S   65 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8235 (mm-30)
REVERT: U    1 MET cc_start: 0.7962 (tpp) cc_final: 0.7000 (ppp)
REVERT: W   30 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7165 (mp0)
REVERT: X   27 MET cc_start: 0.8857 (ttp) cc_final: 0.8521 (ttm)
  outliers start: 16
  outliers final: 10
  residues processed: 538
  average time/residue: 0.1534
  time to fit residues: 113.5498
Evaluate side-chains
  537 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 525
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 MET
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain E residue    3 MET
Chi-restraints excluded: chain M residue    3 MET
Chi-restraints excluded: chain N residue   85 GLU
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain O residue   43 ARG
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain U residue   57 LEU
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Chi-restraints excluded: chain W residue   15 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 127 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0770
   chunk 31 optimal weight:    0.0000
   chunk 90 optimal weight:    0.0270
   chunk 116 optimal weight:    4.9990
   chunk 158 optimal weight:    3.9990
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.6204

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

Flipped N/Q/H residues before XYZ refinement:
** F  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 ASN
** L  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  51 HIS
** N  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  51 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.161453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.132364 restraints weight = 19569.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.32
r_work: 0.3445 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16737  Z= 0.132
  Angle     :  0.654  10.419  22491  Z= 0.345
  Chirality :  0.041   0.256   2310
  Planarity :  0.005   0.064   2877
  Dihedral  :  3.795  16.468   2163
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 18.69 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.18), residues: 1953
  helix:  1.02 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.18 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG Q  89 
 TYR   0.012   0.001   TYR F  32 
 PHE   0.007   0.001   PHE F  25 
 TRP   0.011   0.001   TRP S  94 
 HIS   0.015   0.001   HIS F  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (16737)
  covalent geometry    : angle       0.65389 (22491)
  hydrogen bonds       : bond        0.03702 (  939)
  hydrogen bonds       : angle       4.48907 ( 2817)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  547 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 535
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7460 (tpt) cc_final: 0.7111 (tmm)
REVERT: C   30 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7061 (mp0)
REVERT: C   31 ASP cc_start: 0.7546 (m-30) cc_final: 0.7292 (m-30)
REVERT: D    1 MET cc_start: 0.8039 (tmm) cc_final: 0.7586 (tpp)
REVERT: D   16 ASP cc_start: 0.8462 (t70) cc_final: 0.8044 (t0)
REVERT: D   86 LYS cc_start: 0.8429 (mptt) cc_final: 0.7704 (mtpp)
REVERT: E    3 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5551 (tmm)
REVERT: F    1 MET cc_start: 0.7024 (tmm) cc_final: 0.6466 (mtm)
REVERT: G   43 ARG cc_start: 0.8738 (mtp180) cc_final: 0.8460 (mtp180)
REVERT: G   65 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8127 (mm-30)
REVERT: I    1 MET cc_start: 0.7827 (tpt) cc_final: 0.7549 (tpp)
REVERT: I   43 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8464 (mmm-85)
REVERT: K    1 MET cc_start: 0.6802 (tmm) cc_final: 0.5946 (pmm)
REVERT: K    3 MET cc_start: 0.7065 (ppp) cc_final: 0.6238 (ppp)
REVERT: L   23 LYS cc_start: 0.8754 (mttm) cc_final: 0.8436 (ttpt)
REVERT: M    3 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.5576 (tmm)
REVERT: M   13 TYR cc_start: 0.8760 (m-10) cc_final: 0.8259 (m-10)
REVERT: O   62 ASN cc_start: 0.8492 (m-40) cc_final: 0.8206 (m110)
REVERT: O   64 GLU cc_start: 0.8111 (mp0) cc_final: 0.7870 (mt-10)
REVERT: O   65 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: O   89 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7828 (mtm110)
REVERT: S   64 GLU cc_start: 0.8090 (mp0) cc_final: 0.7866 (mt-10)
REVERT: S   65 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8040 (mm-30)
REVERT: U    1 MET cc_start: 0.7749 (tpp) cc_final: 0.6989 (ppp)
REVERT: U   58 MET cc_start: 0.8726 (mtp) cc_final: 0.8489 (ttm)
REVERT: W   30 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6976 (mp0)
REVERT: X   15 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8424 (mm-30)
REVERT: X   27 MET cc_start: 0.8863 (ttp) cc_final: 0.8550 (ttm)
REVERT: X   43 ARG cc_start: 0.8704 (tpp80) cc_final: 0.8406 (tpp-160)
  outliers start: 12
  outliers final: 8
  residues processed: 536
  average time/residue: 0.1445
  time to fit residues: 106.2795
Evaluate side-chains
  537 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 527
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 MET
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain E residue    3 MET
Chi-restraints excluded: chain M residue    3 MET
Chi-restraints excluded: chain O residue   15 GLU
Chi-restraints excluded: chain O residue   43 ARG
Chi-restraints excluded: chain S residue   27 MET
Chi-restraints excluded: chain V residue   27 MET
Chi-restraints excluded: chain W residue    6 THR
Chi-restraints excluded: chain W residue   15 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 162 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 181 optimal weight:    8.9990
   chunk 147 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 120 optimal weight:    6.9990
   chunk 116 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 146 optimal weight:    0.8980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** F  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.159987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.130715 restraints weight = 19739.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.30
r_work: 0.3434 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  16737  Z= 0.145
  Angle     :  0.667  11.672  22491  Z= 0.351
  Chirality :  0.041   0.263   2310
  Planarity :  0.005   0.062   2877
  Dihedral  :  3.780  15.858   2163
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 18.75 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.18), residues: 1953
  helix:  1.04 (0.13), residues: 1386
  sheet:  None (None), residues: 0
  loop : -1.14 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG Q  89 
 TYR   0.016   0.001   TYR K  32 
 PHE   0.009   0.001   PHE N  25 
 TRP   0.011   0.001   TRP S  94 
 HIS   0.016   0.002   HIS F  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (16737)
  covalent geometry    : angle       0.66747 (22491)
  hydrogen bonds       : bond        0.03912 (  939)
  hydrogen bonds       : angle       4.49950 ( 2817)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3734.09 seconds
wall clock time: 64 minutes 51.45 seconds (3891.45 seconds total)