Starting phenix.real_space_refine
on Sat Aug 23 00:59:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dz5_27789/08_2025/8dz5_27789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dz5_27789/08_2025/8dz5_27789.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dz5_27789/08_2025/8dz5_27789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dz5_27789/08_2025/8dz5_27789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dz5_27789/08_2025/8dz5_27789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dz5_27789/08_2025/8dz5_27789.cif"
  }
  resolution = 3.84
  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=  -0.002 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    5655      2.51       5
     N    1530      2.21       5
     O    1730      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.00s

  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: 8950
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "I"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 280
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 10, 'TRANS': 29}
    Chain: "H"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "B"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "D"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "E"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "F"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "M"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "N"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
  Time building chain proxies: 1.95, per 1000 atoms: 0.22
  Number of scatterers: 8950
  At special positions: 0
  Unit cell: (72.45, 112.7, 115, 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      35     16.00
     O    1730      8.00
     N    1530      7.00
     C    5655      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.03

  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: 0.49
  Conformation dependent library (CDL) restraints added in 376.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 31 sheets defined
      8.5% alpha, 41.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.520A  pdb=" N   GLN H  64 " --> pdb=" O   ASP H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.699A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.701A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 61 through 64
    Processing helix  chain 'A' and resid 73 through 75
      No H-bonds generated for 'chain 'A' and resid 73 through 75'
    Processing helix  chain 'A' and resid 83 through 87
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.594A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 61 through 64
      removed outlier: 3.601A  pdb=" N   GLN C  64 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 61 through 64'
    Processing helix  chain 'C' and resid 83 through 87
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.565A  pdb=" N   PHE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 61 through 64
      removed outlier: 3.532A  pdb=" N   GLN E  64 " --> pdb=" O   ASP E  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 61 through 64'
    Processing helix  chain 'E' and resid 83 through 87
    Processing helix  chain 'F' and resid 79 through 83
      removed outlier: 3.773A  pdb=" N   PHE F  83 " --> pdb=" O   PRO F  80 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 28 through 32
    Processing helix  chain 'M' and resid 61 through 64
      removed outlier: 3.556A  pdb=" N   GLN M  64 " --> pdb=" O   ASP M  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 61 through 64'
    Processing helix  chain 'M' and resid 83 through 87
    Processing helix  chain 'N' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.547A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.389A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 109 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA H  93 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   MET H  34 " --> pdb=" O   ILE H  50 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ILE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.389A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 109 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   CYS H  92 " --> pdb=" O   TRP H 102 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   TRP H 102 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LYS H  94 " --> pdb=" O   ASP H 100C" (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.703A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA6, first strand: chain 'L' and resid 33 through 35
      removed outlier: 4.151A  pdb=" N   GLN L  89 " --> pdb=" O   ALA L  34 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.916A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.275A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   MET A  34 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ILE A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.275A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   CYS A  92 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   TRP A 102 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LYS A  94 " --> pdb=" O   ASP A 100C" (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.805A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 53 through 54
      removed outlier: 6.554A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLN B  89 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.732A  pdb=" N   SER C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU C  80 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER C  70 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.788A  pdb=" N   ALA C  93 " --> pdb=" O   HIS C  35 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   MET C  34 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   ILE C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.785A  pdb=" N   CYS C  92 " --> pdb=" O   TRP C 102 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   TRP C 102 " --> pdb=" O   CYS C  92 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS C  94 " --> pdb=" O   ASP C 100C" (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7
    Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.535A  pdb=" N   THR D 102 " --> pdb=" O   TYR D  86 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37
      removed outlier: 6.432A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN D  37 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.937A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU E  80 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 11
      removed outlier: 3.509A  pdb=" N   ALA E  93 " --> pdb=" O   HIS E  35 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   MET E  34 " --> pdb=" O   ILE E  50 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ILE E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 11
      removed outlier: 6.591A  pdb=" N   CYS E  92 " --> pdb=" O   TRP E 102 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TRP E 102 " --> pdb=" O   CYS E  92 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS E  94 " --> pdb=" O   ASP E 100C" (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 7
    Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13
    Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 54
      removed outlier: 6.481A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   TYR F  49 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LEU F  33 " --> pdb=" O   TYR F  49 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLN F  89 " --> pdb=" O   ALA F  34 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'M' and resid 3 through 7
      removed outlier: 3.776A  pdb=" N   SER M  21 " --> pdb=" O   SER M   7 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU M  80 " --> pdb=" O   LEU M  20 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 11
      removed outlier: 6.492A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 109 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   MET M  34 " --> pdb=" O   ILE M  50 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 11
      removed outlier: 6.492A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 109 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   CYS M  92 " --> pdb=" O   TRP M 102 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   TRP M 102 " --> pdb=" O   CYS M  92 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LYS M  94 " --> pdb=" O   ASP M 100C" (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7
    Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13
    Processing sheet with id=AD4, first strand: chain 'N' and resid 53 through 54
      removed outlier: 3.506A  pdb=" N   GLN N  37 " --> pdb=" O   LYS N  45 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU N  47 " --> pdb=" O   TRP N  35 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   TYR N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   LEU N  33 " --> pdb=" O   TYR N  49 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLN N  89 " --> pdb=" O   ALA N  34 " (cutoff:3.500A)

    335 hydrogen bonds defined for protein.
    750 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: 1.11

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2879
        1.34 -     1.46: 2279
        1.46 -     1.58: 3956
        1.58 -     1.70: 0
        1.70 -     1.81: 50
  Bond restraints: 9164
  Sorted by residual:
  bond pdb=" N   GLY F  64 "
       pdb=" CA  GLY F  64 "
    ideal  model  delta    sigma   weight residual
    1.454  1.443  0.012 9.90e-03 1.02e+04 1.35e+00
  bond pdb=" CA  ASP C 100C"
       pdb=" C   ASP C 100C"
    ideal  model  delta    sigma   weight residual
    1.521  1.532 -0.011 9.90e-03 1.02e+04 1.35e+00
  bond pdb=" CB  ASP H 100C"
       pdb=" CG  ASP H 100C"
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  PRO I  50 "
       pdb=" CG  PRO I  50 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 5.00e-02 4.00e+02 1.07e+00
  bond pdb=" CB  GLU N  81 "
       pdb=" CG  GLU N  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.62e-01
  ... (remaining 9159 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 11832
        1.50 -     3.00: 498
        3.00 -     4.50: 76
        4.50 -     6.00: 16
        6.00 -     7.50: 5
  Bond angle restraints: 12427
  Sorted by residual:
  angle pdb=" CA  GLU N 105 "
        pdb=" CB  GLU N 105 "
        pdb=" CG  GLU N 105 "
      ideal   model   delta    sigma   weight residual
     114.10  121.39   -7.29 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" CA  GLU N  81 "
        pdb=" CB  GLU N  81 "
        pdb=" CG  GLU N  81 "
      ideal   model   delta    sigma   weight residual
     114.10  119.55   -5.45 2.00e+00 2.50e-01 7.44e+00
  angle pdb=" N   ILE F  29 "
        pdb=" CA  ILE F  29 "
        pdb=" CB  ILE F  29 "
      ideal   model   delta    sigma   weight residual
     111.64  109.47    2.17 8.20e-01 1.49e+00 7.02e+00
  angle pdb=" N   LYS D  50 "
        pdb=" CA  LYS D  50 "
        pdb=" C   LYS D  50 "
      ideal   model   delta    sigma   weight residual
     112.86  109.71    3.15 1.22e+00 6.72e-01 6.68e+00
  angle pdb=" C   ASP F  17 "
        pdb=" CA  ASP F  17 "
        pdb=" CB  ASP F  17 "
      ideal   model   delta    sigma   weight residual
     109.76  114.84   -5.08 1.99e+00 2.53e-01 6.53e+00
  ... (remaining 12422 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 4789
       17.78 -    35.56: 459
       35.56 -    53.34: 98
       53.34 -    71.11: 26
       71.11 -    88.89: 12
  Dihedral angle restraints: 5384
    sinusoidal: 2100
      harmonic: 3284
  Sorted by residual:
  dihedral pdb=" CB  CYS B  23 "
           pdb=" SG  CYS B  23 "
           pdb=" SG  CYS B  88 "
           pdb=" CB  CYS B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.94   42.94     1      1.00e+01 1.00e-02 2.57e+01
  dihedral pdb=" CB  CYS F  23 "
           pdb=" SG  CYS F  23 "
           pdb=" SG  CYS F  88 "
           pdb=" CB  CYS F  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.77   40.77     1      1.00e+01 1.00e-02 2.33e+01
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  88 "
           pdb=" CB  CYS D  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.86   37.86     1      1.00e+01 1.00e-02 2.02e+01
  ... (remaining 5381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 823
       0.029 -    0.059: 332
       0.059 -    0.088: 81
       0.088 -    0.117: 77
       0.117 -    0.147: 22
  Chirality restraints: 1335
  Sorted by residual:
  chirality pdb=" CA  VAL A  40 "
            pdb=" N   VAL A  40 "
            pdb=" C   VAL A  40 "
            pdb=" CB  VAL A  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" CA  ASP C 100C"
            pdb=" N   ASP C 100C"
            pdb=" C   ASP C 100C"
            pdb=" CB  ASP C 100C"
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CG  LEU D  33 "
            pdb=" CB  LEU D  33 "
            pdb=" CD1 LEU D  33 "
            pdb=" CD2 LEU D  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 4.82e-01
  ... (remaining 1332 not shown)

  Planarity restraints: 1594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  40 "   -0.054 5.00e-02 4.00e+02   8.11e-02 1.05e+01
        pdb=" N   PRO A  41 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A  41 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A  41 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR N  91 "    0.016 2.00e-02 2.50e+03   1.29e-02 3.33e+00
        pdb=" CG  TYR N  91 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR N  91 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR N  91 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR N  91 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR N  91 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR N  91 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR N  91 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  39 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.33e+00
        pdb=" N   PRO B  40 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B  40 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  40 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1591 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 431
        2.71 -     3.26: 8584
        3.26 -     3.81: 14663
        3.81 -     4.35: 17872
        4.35 -     4.90: 30731
  Nonbonded interactions: 72281
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 100C"
            pdb=" N   TYR C 101 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" O   TYR H  32 "
            pdb=" NH1 ARG H  71 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   TYR C  32 "
            pdb=" NH1 ARG C  71 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" ND2 ASN I  43 "
            pdb=" O   TYR L  91 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OG1 THR E  28 "
            pdb=" OD2 ASP N   1 "
     model   vdw
     2.247 3.040
  ... (remaining 72276 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 'C'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'L'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.700
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
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   0.052   9174  Z= 0.149
  Angle     :  0.713   7.497  12447  Z= 0.400
  Chirality :  0.042   0.147   1335
  Planarity :  0.004   0.081   1594
  Dihedral  : 15.288  88.892   3274
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 18.34 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.63 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.97 (0.23), residues: 495
  loop :  0.25 (0.28), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  18 
 TYR   0.028   0.002   TYR N  91 
 PHE   0.016   0.002   PHE A  79 
 TRP   0.013   0.001   TRP E 102 
 HIS   0.005   0.002   HIS M  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9164)
  covalent geometry    : angle       0.71256 (12427)
  SS BOND              : bond        0.00192 (   10)
  SS BOND              : angle       1.01381 (   20)
  hydrogen bonds       : bond        0.26958 (  311)
  hydrogen bonds       : angle      11.85273 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.7682 (ptpp) cc_final: 0.7476 (ptpp)
REVERT: A   80 LEU cc_start: 0.7136 (tt) cc_final: 0.6845 (tt)
  outliers start: 6
  outliers final: 5
  residues processed: 138
  average time/residue: 0.0925
  time to fit residues: 16.8586
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  106 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN
D  90 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.088607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.069226 restraints weight = 22217.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.071522 restraints weight = 13742.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.073098 restraints weight = 9869.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.074243 restraints weight = 7783.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.074993 restraints weight = 6513.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9174  Z= 0.228
  Angle     :  0.653   6.739  12447  Z= 0.350
  Chirality :  0.045   0.162   1335
  Planarity :  0.004   0.050   1594
  Dihedral  :  5.596  48.282   1263
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 16.89 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.87 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -1.01 (0.22), residues: 535
  loop :  0.06 (0.28), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  71 
 TYR   0.017   0.002   TYR E  90 
 PHE   0.016   0.002   PHE A  79 
 TRP   0.014   0.002   TRP E 102 
 HIS   0.005   0.002   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 9164)
  covalent geometry    : angle       0.65298 (12427)
  SS BOND              : bond        0.00230 (   10)
  SS BOND              : angle       0.73958 (   20)
  hydrogen bonds       : bond        0.04022 (  311)
  hydrogen bonds       : angle       8.09570 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7113 (ttt-90)
REVERT: A   67 PHE cc_start: 0.7456 (m-10) cc_final: 0.6515 (m-10)
REVERT: B   27 GLN cc_start: 0.7039 (mm110) cc_final: 0.6778 (mm-40)
REVERT: C   45 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7415 (mt)
REVERT: C  100 ASP cc_start: 0.8108 (p0) cc_final: 0.7666 (p0)
REVERT: C  102 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.8656 (m100)
REVERT: E  100 ASP cc_start: 0.8002 (p0) cc_final: 0.7506 (t0)
REVERT: N  105 GLU cc_start: 0.7102 (tp30) cc_final: 0.6356 (tm-30)
  outliers start: 37
  outliers final: 17
  residues processed: 146
  average time/residue: 0.0933
  time to fit residues: 18.4330
Evaluate side-chains
  132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain C residue  102 TRP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 GLN
C  39 GLN
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.085819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.065948 restraints weight = 22317.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.068182 restraints weight = 14016.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.069778 restraints weight = 10228.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.070915 restraints weight = 8109.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.071721 restraints weight = 6815.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   9174  Z= 0.294
  Angle     :  0.686   6.801  12447  Z= 0.368
  Chirality :  0.046   0.155   1335
  Planarity :  0.004   0.042   1594
  Dihedral  :  6.044  58.854   1260
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 16.68 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -1.22 (0.22), residues: 535
  loop : -0.12 (0.28), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  24 
 TYR   0.018   0.003   TYR M  91 
 PHE   0.015   0.002   PHE A  79 
 TRP   0.018   0.002   TRP C 102 
 HIS   0.005   0.002   HIS M  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00679 ( 9164)
  covalent geometry    : angle       0.68634 (12427)
  SS BOND              : bond        0.00175 (   10)
  SS BOND              : angle       0.70122 (   20)
  hydrogen bonds       : bond        0.03914 (  311)
  hydrogen bonds       : angle       7.54417 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 117
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8924 (pttt) cc_final: 0.8439 (pttm)
REVERT: A  100 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.4198 (mp10)
REVERT: B   17 ASP cc_start: 0.7226 (t0) cc_final: 0.6205 (m-30)
REVERT: C   45 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7384 (mt)
REVERT: C  102 TRP cc_start: 0.8936 (OUTLIER) cc_final: 0.8611 (m-10)
REVERT: D   50 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8881 (tppt)
REVERT: E   82 MET cc_start: 0.8512 (mmm) cc_final: 0.8205 (mmt)
REVERT: E  100 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7615 (mp10)
REVERT: M  100 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.6911 (mp10)
REVERT: N   58 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8157 (p)
  outliers start: 51
  outliers final: 35
  residues processed: 156
  average time/residue: 0.0958
  time to fit residues: 20.2353
Evaluate side-chains
  151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 110
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   32 SER
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain C residue  102 TRP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  100 GLN
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   49 TYR
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain M residue  100 GLN
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   31 THR
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   90 GLN
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 83 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN
D  90 GLN
M   3 GLN
N  89 GLN
N  90 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.090126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.070500 restraints weight = 22319.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.072862 restraints weight = 13938.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.074507 restraints weight = 10027.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.075641 restraints weight = 7868.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.076436 restraints weight = 6589.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9174  Z= 0.136
  Angle     :  0.618   8.025  12447  Z= 0.324
  Chirality :  0.044   0.181   1335
  Planarity :  0.004   0.045   1594
  Dihedral  :  5.631  59.476   1260
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.65 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.86 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -1.06 (0.22), residues: 535
  loop :  0.12 (0.28), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG M  83 
 TYR   0.014   0.002   TYR H  32 
 PHE   0.011   0.001   PHE A  79 
 TRP   0.009   0.001   TRP C 102 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9164)
  covalent geometry    : angle       0.61768 (12427)
  SS BOND              : bond        0.00268 (   10)
  SS BOND              : angle       0.88307 (   20)
  hydrogen bonds       : bond        0.03118 (  311)
  hydrogen bonds       : angle       6.99266 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8782 (pttt) cc_final: 0.8364 (pttm)
REVERT: B   17 ASP cc_start: 0.7184 (t0) cc_final: 0.6161 (m-30)
REVERT: B  105 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7877 (mm-30)
REVERT: C   45 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7512 (mt)
REVERT: C   53 ASP cc_start: 0.7398 (p0) cc_final: 0.7170 (p0)
REVERT: C  100 ASP cc_start: 0.7935 (p0) cc_final: 0.7559 (p0)
REVERT: E   53 ASP cc_start: 0.8236 (p0) cc_final: 0.7679 (p0)
REVERT: M   11 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8426 (m)
REVERT: N   58 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (p)
REVERT: N  105 GLU cc_start: 0.6815 (tp30) cc_final: 0.6311 (tm-30)
  outliers start: 34
  outliers final: 21
  residues processed: 146
  average time/residue: 0.1192
  time to fit residues: 22.7201
Evaluate side-chains
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   11 VAL
Chi-restraints excluded: chain M residue   28 THR
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 73 optimal weight:    0.0000
   chunk 16 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
D  90 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.090456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.070805 restraints weight = 21968.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.073116 restraints weight = 13545.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.074750 restraints weight = 9772.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.075928 restraints weight = 7676.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.076674 restraints weight = 6422.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9174  Z= 0.136
  Angle     :  0.599   6.502  12447  Z= 0.315
  Chirality :  0.043   0.147   1335
  Planarity :  0.003   0.031   1594
  Dihedral  :  5.245  59.989   1258
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.82 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.73 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.94 (0.23), residues: 535
  loop :  0.18 (0.28), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG M  83 
 TYR   0.021   0.002   TYR N  36 
 PHE   0.009   0.001   PHE A  79 
 TRP   0.012   0.001   TRP C 102 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9164)
  covalent geometry    : angle       0.59877 (12427)
  SS BOND              : bond        0.00268 (   10)
  SS BOND              : angle       0.87922 (   20)
  hydrogen bonds       : bond        0.02998 (  311)
  hydrogen bonds       : angle       6.69828 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8766 (pttt) cc_final: 0.8329 (pttm)
REVERT: A   67 PHE cc_start: 0.7525 (m-10) cc_final: 0.6653 (m-10)
REVERT: A   82 MET cc_start: 0.6875 (mmm) cc_final: 0.6522 (mmt)
REVERT: B   11 LEU cc_start: 0.7987 (tp) cc_final: 0.7776 (tp)
REVERT: B   17 ASP cc_start: 0.7259 (t0) cc_final: 0.6322 (m-30)
REVERT: B  105 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7826 (mm-30)
REVERT: C   45 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7209 (mt)
REVERT: C   53 ASP cc_start: 0.7309 (p0) cc_final: 0.7050 (p0)
REVERT: E   53 ASP cc_start: 0.8225 (p0) cc_final: 0.7666 (p0)
REVERT: E   82 MET cc_start: 0.8754 (mmt) cc_final: 0.8405 (mmt)
REVERT: M   11 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8407 (m)
REVERT: N   58 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7987 (p)
REVERT: N   90 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7577 (pm20)
REVERT: N  105 GLU cc_start: 0.6965 (tp30) cc_final: 0.6657 (tm-30)
  outliers start: 35
  outliers final: 24
  residues processed: 149
  average time/residue: 0.1090
  time to fit residues: 21.3784
Evaluate side-chains
  146 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   11 VAL
Chi-restraints excluded: chain M residue   28 THR
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   90 GLN
Chi-restraints excluded: chain N residue   91 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    9.9990
   chunk 87 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
M   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.091889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.072302 restraints weight = 21838.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.074651 restraints weight = 13419.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.076346 restraints weight = 9630.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.077532 restraints weight = 7530.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.078311 restraints weight = 6255.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9174  Z= 0.117
  Angle     :  0.597   6.674  12447  Z= 0.312
  Chirality :  0.043   0.211   1335
  Planarity :  0.003   0.029   1594
  Dihedral  :  5.022  57.229   1258
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.93 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.58 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.84 (0.23), residues: 530
  loop :  0.26 (0.28), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG M  83 
 TYR   0.019   0.001   TYR N  36 
 PHE   0.009   0.001   PHE H  52A
 TRP   0.008   0.001   TRP C 102 
 HIS   0.002   0.001   HIS M  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9164)
  covalent geometry    : angle       0.59588 (12427)
  SS BOND              : bond        0.00406 (   10)
  SS BOND              : angle       0.95476 (   20)
  hydrogen bonds       : bond        0.02905 (  311)
  hydrogen bonds       : angle       6.42375 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8770 (pttt) cc_final: 0.8341 (pttm)
REVERT: A   57 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7507 (ptmt)
REVERT: A   67 PHE cc_start: 0.7499 (m-10) cc_final: 0.6662 (m-10)
REVERT: A   82 MET cc_start: 0.6886 (mmm) cc_final: 0.6583 (mmt)
REVERT: B   17 ASP cc_start: 0.7212 (t0) cc_final: 0.6199 (m-30)
REVERT: B   24 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7602 (ttm-80)
REVERT: C   45 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7085 (mt)
REVERT: C   53 ASP cc_start: 0.7198 (p0) cc_final: 0.6965 (p0)
REVERT: C  100 ASP cc_start: 0.7843 (p0) cc_final: 0.7622 (p0)
REVERT: E   53 ASP cc_start: 0.8222 (p0) cc_final: 0.7666 (p0)
REVERT: E   82 MET cc_start: 0.8569 (mmt) cc_final: 0.8195 (mmt)
REVERT: M   11 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8388 (m)
  outliers start: 36
  outliers final: 24
  residues processed: 156
  average time/residue: 0.0983
  time to fit residues: 20.3967
Evaluate side-chains
  147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   11 VAL
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 83 optimal weight:    0.5980
   chunk 58 optimal weight:   20.0000
   chunk 64 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
D  90 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.090974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.071385 restraints weight = 22124.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.073731 restraints weight = 13557.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.075420 restraints weight = 9710.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.076576 restraints weight = 7587.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.077351 restraints weight = 6337.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9174  Z= 0.146
  Angle     :  0.636  11.510  12447  Z= 0.323
  Chirality :  0.043   0.224   1335
  Planarity :  0.003   0.037   1594
  Dihedral  :  5.029  55.033   1258
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.96 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.82 (0.23), residues: 530
  loop :  0.30 (0.28), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  18 
 TYR   0.019   0.002   TYR B  91 
 PHE   0.009   0.001   PHE A  79 
 TRP   0.010   0.001   TRP D  35 
 HIS   0.004   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9164)
  covalent geometry    : angle       0.63542 (12427)
  SS BOND              : bond        0.00265 (   10)
  SS BOND              : angle       1.01097 (   20)
  hydrogen bonds       : bond        0.02873 (  311)
  hydrogen bonds       : angle       6.39507 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8797 (pttt) cc_final: 0.8391 (pttm)
REVERT: A   57 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7497 (ptmt)
REVERT: A   67 PHE cc_start: 0.7523 (m-10) cc_final: 0.6634 (m-10)
REVERT: A   82 MET cc_start: 0.6915 (mmm) cc_final: 0.6606 (mmt)
REVERT: B   17 ASP cc_start: 0.7303 (t0) cc_final: 0.6376 (m-30)
REVERT: C   45 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7141 (mt)
REVERT: C   53 ASP cc_start: 0.7277 (p0) cc_final: 0.7036 (p0)
REVERT: C  100 ASP cc_start: 0.7907 (p0) cc_final: 0.7629 (p0)
REVERT: E   53 ASP cc_start: 0.8253 (p0) cc_final: 0.7679 (p0)
REVERT: E   82 MET cc_start: 0.8495 (mmt) cc_final: 0.8280 (mmt)
REVERT: M   11 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8434 (m)
REVERT: M   99 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6372 (tt0)
REVERT: N   30 SER cc_start: 0.7325 (OUTLIER) cc_final: 0.7016 (p)
  outliers start: 39
  outliers final: 26
  residues processed: 151
  average time/residue: 0.1043
  time to fit residues: 20.7812
Evaluate side-chains
  147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   11 VAL
Chi-restraints excluded: chain M residue   28 THR
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   99 GLU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 54 optimal weight:    9.9990
   chunk 57 optimal weight:    0.3980
   chunk 34 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 103 optimal weight:    0.2980
   chunk 104 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.090743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.070880 restraints weight = 21718.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.073283 restraints weight = 13459.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.074945 restraints weight = 9680.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.076071 restraints weight = 7633.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.076841 restraints weight = 6413.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9174  Z= 0.130
  Angle     :  0.626   8.818  12447  Z= 0.321
  Chirality :  0.043   0.161   1335
  Planarity :  0.003   0.028   1594
  Dihedral  :  4.995  53.578   1258
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 19.17 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.48 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.79 (0.23), residues: 530
  loop :  0.35 (0.28), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG M  83 
 TYR   0.020   0.001   TYR B  91 
 PHE   0.009   0.001   PHE A  79 
 TRP   0.009   0.001   TRP D  35 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9164)
  covalent geometry    : angle       0.62504 (12427)
  SS BOND              : bond        0.00260 (   10)
  SS BOND              : angle       1.05517 (   20)
  hydrogen bonds       : bond        0.02818 (  311)
  hydrogen bonds       : angle       6.24481 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 125
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8775 (pttt) cc_final: 0.8393 (pttm)
REVERT: A   57 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7499 (ptmt)
REVERT: A   67 PHE cc_start: 0.7609 (m-10) cc_final: 0.6631 (m-10)
REVERT: A   75 LYS cc_start: 0.7512 (ptpp) cc_final: 0.7292 (ptpp)
REVERT: B   17 ASP cc_start: 0.7258 (t0) cc_final: 0.6324 (m-30)
REVERT: B   87 TYR cc_start: 0.7250 (m-80) cc_final: 0.7021 (m-10)
REVERT: B  105 GLU cc_start: 0.6481 (tm-30) cc_final: 0.6237 (tm-30)
REVERT: C   45 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7090 (mt)
REVERT: C   53 ASP cc_start: 0.7243 (p0) cc_final: 0.7002 (p0)
REVERT: D   58 VAL cc_start: 0.8428 (t) cc_final: 0.8214 (p)
REVERT: E   53 ASP cc_start: 0.8227 (p0) cc_final: 0.7657 (p0)
REVERT: M   11 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8405 (m)
REVERT: N   30 SER cc_start: 0.7293 (OUTLIER) cc_final: 0.6974 (p)
REVERT: N   58 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7925 (p)
  outliers start: 40
  outliers final: 27
  residues processed: 158
  average time/residue: 0.0993
  time to fit residues: 21.2922
Evaluate side-chains
  151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   11 VAL
Chi-restraints excluded: chain M residue   28 THR
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   99 GLU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    0.4980
   chunk 98 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 88 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
F  90 GLN
M   3 GLN
** N  90 GLN ** 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 = 0.3530 r_free = 0.3530 target = 0.090071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.070404 restraints weight = 22060.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.072691 restraints weight = 13744.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.074293 restraints weight = 9921.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.075336 restraints weight = 7858.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.076150 restraints weight = 6654.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9174  Z= 0.192
  Angle     :  0.676  10.092  12447  Z= 0.346
  Chirality :  0.044   0.244   1335
  Planarity :  0.004   0.048   1594
  Dihedral  :  5.225  52.298   1258
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 19.17 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.58 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.76 (0.23), residues: 520
  loop :  0.15 (0.28), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  18 
 TYR   0.016   0.002   TYR B  91 
 PHE   0.016   0.001   PHE A  67 
 TRP   0.014   0.002   TRP D  35 
 HIS   0.006   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 9164)
  covalent geometry    : angle       0.67525 (12427)
  SS BOND              : bond        0.00247 (   10)
  SS BOND              : angle       1.14506 (   20)
  hydrogen bonds       : bond        0.03006 (  311)
  hydrogen bonds       : angle       6.48513 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8834 (pttt) cc_final: 0.8418 (pttm)
REVERT: A   57 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7456 (ptmt)
REVERT: B   17 ASP cc_start: 0.7415 (t0) cc_final: 0.6422 (m-30)
REVERT: B  105 GLU cc_start: 0.6283 (tm-30) cc_final: 0.5988 (tm-30)
REVERT: C   45 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7243 (mt)
REVERT: C   53 ASP cc_start: 0.7327 (p0) cc_final: 0.7118 (p0)
REVERT: E   53 ASP cc_start: 0.8315 (p0) cc_final: 0.7993 (p0)
REVERT: N   30 SER cc_start: 0.7315 (OUTLIER) cc_final: 0.7039 (p)
REVERT: N   58 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.8032 (p)
  outliers start: 41
  outliers final: 32
  residues processed: 152
  average time/residue: 0.0945
  time to fit residues: 19.3339
Evaluate side-chains
  151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   28 THR
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   99 GLU
Chi-restraints excluded: chain M residue  102 TRP
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 67 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
M   3 GLN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.087474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.067617 restraints weight = 22016.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.069926 restraints weight = 13683.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.071496 restraints weight = 9881.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.072641 restraints weight = 7839.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.073401 restraints weight = 6599.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9174  Z= 0.241
  Angle     :  0.722  10.365  12447  Z= 0.367
  Chirality :  0.045   0.243   1335
  Planarity :  0.004   0.031   1594
  Dihedral  :  5.496  51.803   1258
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 19.59 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.78 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.90 (0.22), residues: 525
  loop :  0.03 (0.28), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG M  83 
 TYR   0.018   0.002   TYR M  91 
 PHE   0.014   0.002   PHE A  79 
 TRP   0.022   0.002   TRP D  35 
 HIS   0.006   0.002   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 9164)
  covalent geometry    : angle       0.72082 (12427)
  SS BOND              : bond        0.00272 (   10)
  SS BOND              : angle       1.29947 (   20)
  hydrogen bonds       : bond        0.03166 (  311)
  hydrogen bonds       : angle       6.73664 (  750)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8872 (pttt) cc_final: 0.8391 (pttm)
REVERT: A   57 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7452 (ptmt)
REVERT: B   17 ASP cc_start: 0.7525 (t0) cc_final: 0.6412 (m-30)
REVERT: B  105 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5948 (tm-30)
REVERT: C   45 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7642 (mt)
REVERT: E   53 ASP cc_start: 0.8380 (p0) cc_final: 0.8046 (p0)
REVERT: M   82 SER cc_start: 0.9306 (m) cc_final: 0.9081 (p)
REVERT: N   58 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8139 (p)
  outliers start: 38
  outliers final: 30
  residues processed: 147
  average time/residue: 0.0875
  time to fit residues: 17.4562
Evaluate side-chains
  148 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   28 THR
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   99 GLU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 104 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 101 optimal weight:    0.6980
   chunk 17 optimal weight:   10.0000
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
M   3 GLN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.089822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.070116 restraints weight = 21847.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.072397 restraints weight = 13716.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.073980 restraints weight = 9978.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.075067 restraints weight = 7901.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.075874 restraints weight = 6660.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9174  Z= 0.177
  Angle     :  0.700  10.042  12447  Z= 0.354
  Chirality :  0.044   0.228   1335
  Planarity :  0.003   0.029   1594
  Dihedral  :  5.341  52.417   1258
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.79 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.84 (0.23), residues: 520
  loop :  0.06 (0.28), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG M  83 
 TYR   0.024   0.002   TYR B  91 
 PHE   0.019   0.001   PHE E  67 
 TRP   0.016   0.001   TRP D  35 
 HIS   0.005   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 9164)
  covalent geometry    : angle       0.69809 (12427)
  SS BOND              : bond        0.00282 (   10)
  SS BOND              : angle       1.30985 (   20)
  hydrogen bonds       : bond        0.02990 (  311)
  hydrogen bonds       : angle       6.60860 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1369.26 seconds
wall clock time: 24 minutes 23.87 seconds (1463.87 seconds total)