Starting phenix.real_space_refine
on Wed Jul 30 12:21:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d64_27216/07_2025/8d64_27216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d64_27216/07_2025/8d64_27216.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d64_27216/07_2025/8d64_27216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d64_27216/07_2025/8d64_27216.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d64_27216/07_2025/8d64_27216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d64_27216/07_2025/8d64_27216.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
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    8175      2.51       5
     N    2085      2.21       5
     O    2250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12545
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'DHL': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.09, per 1000 atoms: 0.41
  Number of scatterers: 12545
  At special positions: 0
  Unit cell: (90.2, 90.2, 123.2, 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    2250      8.00
     N    2085      7.00
     C    8175      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.90
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 15 sheets defined
      32.5% alpha, 36.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 69
      removed outlier: 3.654A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN A  69 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 249
    Processing helix  chain 'A' and resid 260 through 286
    Processing helix  chain 'A' and resid 302 through 317
    Processing helix  chain 'B' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN B  69 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU B 212 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 249
    Processing helix  chain 'B' and resid 260 through 286
    Processing helix  chain 'B' and resid 302 through 317
    Processing helix  chain 'C' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN C  69 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 249
    Processing helix  chain 'C' and resid 260 through 286
    Processing helix  chain 'C' and resid 302 through 317
    Processing helix  chain 'D' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASN D  69 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
      removed outlier: 3.530A  pdb=" N   LEU D 212 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 249
    Processing helix  chain 'D' and resid 260 through 286
    Processing helix  chain 'D' and resid 302 through 317
    Processing helix  chain 'E' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN E  69 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU E 212 " --> pdb=" O   PHE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 249
    Processing helix  chain 'E' and resid 260 through 286
    Processing helix  chain 'E' and resid 302 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 5.294A  pdb=" N   THR A  87 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU A 107 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   ASN A  89 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   THR A  32 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   VAL A  26 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   TYR A  38 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE A  20 " --> pdb=" O   TYR A  38 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   VAL A  40 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN A  42 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL A  16 " --> pdb=" O   GLN A  42 " (cutoff:3.500A)
      removed outlier: 8.728A  pdb=" N   THR A  44 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL A  14 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58
      removed outlier: 5.293A  pdb=" N   THR B  87 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU B 107 " --> pdb=" O   THR B  87 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   ASN B  89 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR B  32 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   VAL B  26 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   TYR B  38 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE B  20 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL B  40 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN B  42 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL B  16 " --> pdb=" O   GLN B  42 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   THR B  44 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   VAL B  14 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58
      removed outlier: 5.293A  pdb=" N   THR C  87 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU C 107 " --> pdb=" O   THR C  87 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASN C  89 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL C  26 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   TYR C  38 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE C  20 " --> pdb=" O   TYR C  38 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL C  40 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN C  42 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   VAL C  16 " --> pdb=" O   GLN C  42 " (cutoff:3.500A)
      removed outlier: 8.728A  pdb=" N   THR C  44 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL C  14 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58
      removed outlier: 5.294A  pdb=" N   THR D  87 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU D 107 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASN D  89 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR D  32 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL D  26 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   TYR D  38 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ILE D  20 " --> pdb=" O   TYR D  38 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   VAL D  40 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN D  42 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL D  16 " --> pdb=" O   GLN D  42 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   THR D  44 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL D  14 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.522A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.522A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58
      removed outlier: 5.293A  pdb=" N   THR E  87 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU E 107 " --> pdb=" O   THR E  87 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASN E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR E  32 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   VAL E  26 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   TYR E  38 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE E  20 " --> pdb=" O   TYR E  38 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL E  40 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN E  42 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   VAL E  16 " --> pdb=" O   GLN E  42 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   THR E  44 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL E  14 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1830 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: 3.98

  Time building geometry restraints manager: 3.31 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: 3947
        1.34 -     1.46: 2403
        1.46 -     1.57: 6475
        1.57 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" N   ASP D 158 "
       pdb=" CA  ASP D 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 6.30e-03 2.52e+04 2.20e+01
  bond pdb=" N   ASP E 158 "
       pdb=" CA  ASP E 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.029 6.30e-03 2.52e+04 2.19e+01
  bond pdb=" N   ASP A 158 "
       pdb=" CA  ASP A 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.029 6.30e-03 2.52e+04 2.15e+01
  bond pdb=" N   ASP B 158 "
       pdb=" CA  ASP B 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 6.30e-03 2.52e+04 2.11e+01
  bond pdb=" N   ASP C 158 "
       pdb=" CA  ASP C 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 6.30e-03 2.52e+04 2.08e+01
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 16567
        1.52 -     3.05: 802
        3.05 -     4.57: 121
        4.57 -     6.10: 25
        6.10 -     7.62: 30
  Bond angle restraints: 17545
  Sorted by residual:
  angle pdb=" C   ASP B 158 "
        pdb=" CA  ASP B 158 "
        pdb=" CB  ASP B 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.76    5.78 1.46e+00 4.69e-01 1.57e+01
  angle pdb=" C   ASP E 158 "
        pdb=" CA  ASP E 158 "
        pdb=" CB  ASP E 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.79    5.75 1.46e+00 4.69e-01 1.55e+01
  angle pdb=" C   ASP C 158 "
        pdb=" CA  ASP C 158 "
        pdb=" CB  ASP C 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.80    5.74 1.46e+00 4.69e-01 1.55e+01
  angle pdb=" C   ASP A 158 "
        pdb=" CA  ASP A 158 "
        pdb=" CB  ASP A 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.81    5.73 1.46e+00 4.69e-01 1.54e+01
  angle pdb=" C   ASP D 158 "
        pdb=" CA  ASP D 158 "
        pdb=" CB  ASP D 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.82    5.72 1.46e+00 4.69e-01 1.54e+01
  ... (remaining 17540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 6702
       16.95 -    33.89: 703
       33.89 -    50.84: 100
       50.84 -    67.78: 15
       67.78 -    84.73: 10
  Dihedral angle restraints: 7530
    sinusoidal: 3025
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  LEU C 118 "
           pdb=" C   LEU C 118 "
           pdb=" N   PHE C 119 "
           pdb=" CA  PHE C 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.43  -28.57     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  LEU E 118 "
           pdb=" C   LEU E 118 "
           pdb=" N   PHE E 119 "
           pdb=" CA  PHE E 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.45  -28.55     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  LEU A 118 "
           pdb=" C   LEU A 118 "
           pdb=" N   PHE A 119 "
           pdb=" CA  PHE A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.45  -28.55     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1323
       0.050 -    0.100: 453
       0.100 -    0.150: 137
       0.150 -    0.200: 26
       0.200 -    0.250: 11
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CA  GLU B 156 "
            pdb=" N   GLU B 156 "
            pdb=" C   GLU B 156 "
            pdb=" CB  GLU B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  GLU A 156 "
            pdb=" N   GLU A 156 "
            pdb=" C   GLU A 156 "
            pdb=" CB  GLU A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  GLU E 156 "
            pdb=" N   GLU E 156 "
            pdb=" C   GLU E 156 "
            pdb=" CB  GLU E 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D  54 "    0.039 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO D  55 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO D  55 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D  55 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  54 "   -0.039 5.00e-02 4.00e+02   5.87e-02 5.52e+00
        pdb=" N   PRO C  55 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E  54 "    0.039 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO E  55 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO E  55 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO E  55 "    0.033 5.00e-02 4.00e+02
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3289
        2.80 -     3.32: 10426
        3.32 -     3.85: 20050
        3.85 -     4.37: 24068
        4.37 -     4.90: 43065
  Nonbonded interactions: 100898
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  59 "
            pdb=" OG  SER B 134 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG  SER A 227 "
            pdb=" CG  GLU A 230 "
     model   vdw
     2.289 3.440
  nonbonded pdb=" OG  SER C 227 "
            pdb=" CG  GLU C 230 "
     model   vdw
     2.289 3.440
  nonbonded pdb=" OG  SER E 227 "
            pdb=" CG  GLU E 230 "
     model   vdw
     2.289 3.440
  nonbonded pdb=" OG  SER B 227 "
            pdb=" CG  GLU B 230 "
     model   vdw
     2.289 3.440
  ... (remaining 100893 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     26.550
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
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      :  0.007   0.045  12880  Z= 0.331
  Angle     :  0.809   7.624  17545  Z= 0.470
  Chirality :  0.058   0.250   1950
  Planarity :  0.006   0.059   2235
  Dihedral  : 13.690  84.726   4620
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.18), residues: 1525
  helix: -1.79 (0.18), residues: 535
  sheet: -1.46 (0.22), residues: 505
  loop : -3.92 (0.20), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 206 
 HIS   0.005   0.001   HIS D 177 
 PHE   0.014   0.002   PHE C 106 
 TYR   0.016   0.002   TYR B 245 
 ARG   0.003   0.000   ARG E 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11028 (  575)
  hydrogen bonds       : angle       5.98952 ( 1830)
  covalent geometry    : bond        0.00709 (12880)
  covalent geometry    : angle       0.80887 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.352 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.8893 (m-80) cc_final: 0.8508 (m-80)
REVERT: B  131 GLU cc_start: 0.8794 (tt0) cc_final: 0.8481 (tt0)
REVERT: C   38 TYR cc_start: 0.8912 (m-80) cc_final: 0.8611 (m-80)
REVERT: C   90 LYS cc_start: 0.8893 (pttt) cc_final: 0.8600 (pttm)
REVERT: C  146 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7878 (mm-40)
REVERT: D   38 TYR cc_start: 0.8771 (m-80) cc_final: 0.8506 (m-80)
REVERT: E   65 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8266 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2824
  time to fit residues: 76.4881
Evaluate side-chains
  121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 117 optimal weight:   20.0000
   chunk 45 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 139 GLN
A 182 GLN
B 139 GLN
C 139 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.152672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.126390 restraints weight = 14171.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 0.80
r_work: 0.3066 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 2.31 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  12880  Z= 0.114
  Angle     :  0.539   5.848  17545  Z= 0.283
  Chirality :  0.046   0.147   1950
  Planarity :  0.004   0.046   2235
  Dihedral  :  4.958  20.817   1690
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.85 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.20), residues: 1525
  helix:  0.04 (0.21), residues: 510
  sheet: -0.62 (0.27), residues: 395
  loop : -3.02 (0.20), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 206 
 HIS   0.004   0.001   HIS C 177 
 PHE   0.011   0.001   PHE D 247 
 TYR   0.011   0.001   TYR A 245 
 ARG   0.008   0.001   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  575)
  hydrogen bonds       : angle       4.37303 ( 1830)
  covalent geometry    : bond        0.00254 (12880)
  covalent geometry    : angle       0.53936 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 165
  time to evaluate  : 1.528 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.9054 (ptpp) cc_final: 0.8827 (pttm)
REVERT: A  245 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.6712 (t80)
REVERT: B   38 TYR cc_start: 0.9028 (m-80) cc_final: 0.8687 (m-80)
REVERT: C   38 TYR cc_start: 0.9005 (m-80) cc_final: 0.8725 (m-80)
REVERT: C   90 LYS cc_start: 0.9025 (pttt) cc_final: 0.8787 (pttm)
REVERT: C  146 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8256 (mm-40)
REVERT: D   38 TYR cc_start: 0.9019 (m-80) cc_final: 0.8735 (m-80)
REVERT: D   65 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.8168 (mtm110)
REVERT: E   65 ARG cc_start: 0.8703 (mtp-110) cc_final: 0.8502 (mtm110)
REVERT: E  245 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.6897 (t80)
  outliers start: 31
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2629
  time to fit residues: 70.4931
Evaluate side-chains
  159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 146 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    4.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.144265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.105204 restraints weight = 14541.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.60
r_work: 0.2873 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054  12880  Z= 0.315
  Angle     :  0.680   7.195  17545  Z= 0.356
  Chirality :  0.053   0.146   1950
  Planarity :  0.005   0.048   2235
  Dihedral  :  5.640  29.176   1690
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.55 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.21), residues: 1525
  helix:  0.47 (0.22), residues: 530
  sheet: -0.41 (0.24), residues: 485
  loop : -3.50 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 224 
 HIS   0.009   0.002   HIS C 177 
 PHE   0.020   0.002   PHE D 121 
 TYR   0.022   0.002   TYR C 245 
 ARG   0.008   0.001   ARG C  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05028 (  575)
  hydrogen bonds       : angle       4.68449 ( 1830)
  covalent geometry    : bond        0.00783 (12880)
  covalent geometry    : angle       0.68040 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 1.443 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.9225 (m-80) cc_final: 0.9017 (m-80)
REVERT: C   38 TYR cc_start: 0.9166 (m-80) cc_final: 0.8901 (m-80)
REVERT: C   90 LYS cc_start: 0.9160 (pttt) cc_final: 0.8873 (pttm)
REVERT: C  146 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8377 (mm-40)
REVERT: D   65 ARG cc_start: 0.8768 (mtp-110) cc_final: 0.8555 (mtm110)
  outliers start: 37
  outliers final: 29
  residues processed: 162
  average time/residue: 0.2657
  time to fit residues: 61.1149
Evaluate side-chains
  161 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  107 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 116 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 129 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 51 optimal weight:    9.9990
   chunk 90 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 139 GLN
A 182 GLN
** A 200 ASN ** 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 = 0.3601 r_free = 0.3601 target = 0.149600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.111842 restraints weight = 14212.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.23
r_work: 0.2992 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12880  Z= 0.110
  Angle     :  0.519   5.569  17545  Z= 0.271
  Chirality :  0.046   0.146   1950
  Planarity :  0.004   0.043   2235
  Dihedral  :  4.850  20.471   1690
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.98 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.21), residues: 1525
  helix:  1.07 (0.22), residues: 530
  sheet: -0.27 (0.28), residues: 395
  loop : -2.68 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 206 
 HIS   0.004   0.001   HIS B 177 
 PHE   0.010   0.001   PHE E 106 
 TYR   0.013   0.001   TYR C 245 
 ARG   0.005   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  575)
  hydrogen bonds       : angle       4.15777 ( 1830)
  covalent geometry    : bond        0.00246 (12880)
  covalent geometry    : angle       0.51912 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 LYS cc_start: 0.9126 (ptpp) cc_final: 0.8890 (pttm)
REVERT: B   38 TYR cc_start: 0.9116 (m-80) cc_final: 0.8820 (m-80)
REVERT: B  245 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.6808 (t80)
REVERT: B  287 GLN cc_start: 0.0752 (OUTLIER) cc_final: 0.0442 (mm110)
REVERT: C   38 TYR cc_start: 0.9096 (m-80) cc_final: 0.8745 (m-80)
REVERT: C  146 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8310 (mm-40)
REVERT: C  245 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.6648 (t80)
REVERT: D   38 TYR cc_start: 0.9021 (m-80) cc_final: 0.8779 (m-80)
REVERT: D   65 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.8495 (mtm110)
REVERT: D  239 MET cc_start: 0.7626 (ttm) cc_final: 0.7426 (mtt)
  outliers start: 34
  outliers final: 26
  residues processed: 177
  average time/residue: 0.2398
  time to fit residues: 61.7589
Evaluate side-chains
  177 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 132 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.145202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.104538 restraints weight = 14325.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.61
r_work: 0.2851 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  12880  Z= 0.263
  Angle     :  0.627   6.027  17545  Z= 0.326
  Chirality :  0.051   0.146   1950
  Planarity :  0.005   0.044   2235
  Dihedral  :  5.292  26.773   1690
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.58 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.22), residues: 1525
  helix:  1.10 (0.23), residues: 530
  sheet: -0.32 (0.27), residues: 425
  loop : -2.94 (0.21), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 206 
 HIS   0.008   0.002   HIS E 177 
 PHE   0.018   0.002   PHE B 121 
 TYR   0.020   0.002   TYR C 245 
 ARG   0.008   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04411 (  575)
  hydrogen bonds       : angle       4.44249 ( 1830)
  covalent geometry    : bond        0.00655 (12880)
  covalent geometry    : angle       0.62669 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 1.301 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.9224 (m-80) cc_final: 0.8946 (m-80)
REVERT: B  124 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7791 (mm-40)
REVERT: B  145 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.8894 (tp)
REVERT: B  287 GLN cc_start: 0.0697 (OUTLIER) cc_final: 0.0328 (mm110)
REVERT: C   38 TYR cc_start: 0.9182 (m-80) cc_final: 0.8876 (m-80)
REVERT: C  146 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8474 (mm-40)
REVERT: D  145 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9118 (tp)
REVERT: E  145 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.8887 (tp)
  outliers start: 37
  outliers final: 31
  residues processed: 164
  average time/residue: 0.2441
  time to fit residues: 57.8199
Evaluate side-chains
  171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   34 LYS
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   chunk 135 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 88 optimal weight:   20.0000
   chunk 132 optimal weight:    0.9990
   chunk 128 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
B  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.147355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.107423 restraints weight = 14459.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.36
r_work: 0.2916 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12880  Z= 0.159
  Angle     :  0.558   5.731  17545  Z= 0.290
  Chirality :  0.047   0.144   1950
  Planarity :  0.004   0.043   2235
  Dihedral  :  5.026  23.637   1690
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.80 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.22), residues: 1525
  helix:  1.28 (0.23), residues: 530
  sheet:  0.23 (0.25), residues: 475
  loop : -3.17 (0.22), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 206 
 HIS   0.005   0.001   HIS C 177 
 PHE   0.013   0.001   PHE C 247 
 TYR   0.016   0.001   TYR C 245 
 ARG   0.011   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  575)
  hydrogen bonds       : angle       4.27223 ( 1830)
  covalent geometry    : bond        0.00381 (12880)
  covalent geometry    : angle       0.55768 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.8878 (tp)
REVERT: B   38 TYR cc_start: 0.9186 (m-80) cc_final: 0.8873 (m-80)
REVERT: B  287 GLN cc_start: 0.0582 (OUTLIER) cc_final: 0.0257 (mm110)
REVERT: C   38 TYR cc_start: 0.9154 (m-80) cc_final: 0.8820 (m-80)
REVERT: C  146 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8411 (mm-40)
REVERT: E  182 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7689 (mp10)
REVERT: E  287 GLN cc_start: 0.1008 (OUTLIER) cc_final: 0.0142 (mm110)
  outliers start: 36
  outliers final: 31
  residues processed: 174
  average time/residue: 0.2551
  time to fit residues: 64.7294
Evaluate side-chains
  178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  182 GLN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 139 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 113 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 146 optimal weight:   10.0000
   chunk 98 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.147809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.110427 restraints weight = 14329.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 1.40
r_work: 0.2929 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12880  Z= 0.178
  Angle     :  0.580  13.745  17545  Z= 0.299
  Chirality :  0.048   0.151   1950
  Planarity :  0.004   0.043   2235
  Dihedral  :  5.036  24.064   1690
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.80 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.22), residues: 1525
  helix:  1.28 (0.23), residues: 530
  sheet:  0.32 (0.25), residues: 475
  loop : -3.16 (0.22), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 206 
 HIS   0.005   0.001   HIS B 177 
 PHE   0.014   0.002   PHE C 247 
 TYR   0.016   0.002   TYR C 245 
 ARG   0.007   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  575)
  hydrogen bonds       : angle       4.27663 ( 1830)
  covalent geometry    : bond        0.00432 (12880)
  covalent geometry    : angle       0.58022 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 143
  time to evaluate  : 1.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.8866 (tp)
REVERT: B   38 TYR cc_start: 0.9166 (m-80) cc_final: 0.8865 (m-80)
REVERT: B   93 MET cc_start: 0.8928 (ttt) cc_final: 0.8700 (mtp)
REVERT: B  145 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.8887 (tp)
REVERT: B  287 GLN cc_start: 0.0715 (OUTLIER) cc_final: 0.0365 (mm110)
REVERT: C   38 TYR cc_start: 0.9137 (m-80) cc_final: 0.8849 (m-80)
REVERT: C  146 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8371 (mm-40)
REVERT: D  145 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9111 (tp)
REVERT: E  145 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.8874 (tp)
REVERT: E  182 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7779 (mp10)
REVERT: E  287 GLN cc_start: 0.1108 (OUTLIER) cc_final: 0.0209 (mm110)
  outliers start: 42
  outliers final: 33
  residues processed: 175
  average time/residue: 0.2347
  time to fit residues: 60.7099
Evaluate side-chains
  183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 143
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  182 GLN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 145 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 113 optimal weight:    8.9990
   chunk 117 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.145471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.110596 restraints weight = 14468.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.50
r_work: 0.2895 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  12880  Z= 0.247
  Angle     :  0.629   9.706  17545  Z= 0.326
  Chirality :  0.050   0.147   1950
  Planarity :  0.005   0.046   2235
  Dihedral  :  5.297  26.937   1690
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.09 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.22), residues: 1525
  helix:  1.17 (0.23), residues: 530
  sheet:  0.28 (0.25), residues: 475
  loop : -3.18 (0.22), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 206 
 HIS   0.006   0.001   HIS E 177 
 PHE   0.016   0.002   PHE E 121 
 TYR   0.021   0.002   TYR C 245 
 ARG   0.008   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04442 (  575)
  hydrogen bonds       : angle       4.45784 ( 1830)
  covalent geometry    : bond        0.00610 (12880)
  covalent geometry    : angle       0.62877 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 139
  time to evaluate  : 1.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.8908 (tp)
REVERT: B   38 TYR cc_start: 0.9195 (m-80) cc_final: 0.8959 (m-80)
REVERT: B  145 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.8894 (tp)
REVERT: B  287 GLN cc_start: 0.0823 (OUTLIER) cc_final: 0.0475 (mm110)
REVERT: C   38 TYR cc_start: 0.9158 (m-80) cc_final: 0.8864 (m-80)
REVERT: C  124 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8522 (mm110)
REVERT: C  146 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8446 (mm-40)
REVERT: D  145 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9115 (tp)
REVERT: E  145 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.8918 (tp)
REVERT: E  182 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7768 (mp10)
  outliers start: 47
  outliers final: 37
  residues processed: 175
  average time/residue: 0.2782
  time to fit residues: 70.5090
Evaluate side-chains
  182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 138
  time to evaluate  : 1.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  124 GLN
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  184 ASN
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  182 GLN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0570
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 86 optimal weight:   10.0000
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
B  62 GLN
D 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.151355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.126005 restraints weight = 14193.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 0.78
r_work: 0.3086 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12880  Z= 0.102
  Angle     :  0.521  10.671  17545  Z= 0.267
  Chirality :  0.046   0.146   1950
  Planarity :  0.004   0.039   2235
  Dihedral  :  4.648  20.013   1690
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.25 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.22), residues: 1525
  helix:  1.44 (0.23), residues: 530
  sheet:  0.62 (0.25), residues: 460
  loop : -3.14 (0.22), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 206 
 HIS   0.004   0.001   HIS B 177 
 PHE   0.012   0.001   PHE E 106 
 TYR   0.008   0.001   TYR E 258 
 ARG   0.008   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (  575)
  hydrogen bonds       : angle       4.05098 ( 1830)
  covalent geometry    : bond        0.00224 (12880)
  covalent geometry    : angle       0.52135 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 151
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 LYS cc_start: 0.9013 (ptpp) cc_final: 0.8791 (pttm)
REVERT: A  138 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8163 (mm110)
REVERT: A  145 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.8807 (tp)
REVERT: B   38 TYR cc_start: 0.9037 (m-80) cc_final: 0.8762 (m-80)
REVERT: B  145 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.8853 (tp)
REVERT: B  287 GLN cc_start: 0.1068 (OUTLIER) cc_final: 0.0739 (mm110)
REVERT: C   38 TYR cc_start: 0.9001 (m-80) cc_final: 0.8703 (m-80)
REVERT: C  146 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8305 (mm-40)
REVERT: D  145 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9052 (tp)
REVERT: E  287 GLN cc_start: 0.1378 (OUTLIER) cc_final: 0.0371 (mm110)
  outliers start: 32
  outliers final: 23
  residues processed: 175
  average time/residue: 0.2323
  time to fit residues: 60.4158
Evaluate side-chains
  171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  184 ASN
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   chunk 122 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 131 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.149234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.116014 restraints weight = 14271.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.00
r_work: 0.3021 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12880  Z= 0.124
  Angle     :  0.538   9.780  17545  Z= 0.275
  Chirality :  0.046   0.144   1950
  Planarity :  0.004   0.053   2235
  Dihedral  :  4.692  20.199   1690
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.69 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.22), residues: 1525
  helix:  1.50 (0.23), residues: 530
  sheet:  0.62 (0.26), residues: 445
  loop : -2.75 (0.23), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 206 
 HIS   0.004   0.001   HIS B 177 
 PHE   0.010   0.001   PHE E 106 
 TYR   0.012   0.001   TYR C 245 
 ARG   0.014   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03357 (  575)
  hydrogen bonds       : angle       4.05637 ( 1830)
  covalent geometry    : bond        0.00291 (12880)
  covalent geometry    : angle       0.53813 (17545)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8262 (mm110)
REVERT: A  145 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.8841 (tp)
REVERT: B   38 TYR cc_start: 0.9072 (m-80) cc_final: 0.8801 (m-80)
REVERT: B  145 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.8850 (tp)
REVERT: B  287 GLN cc_start: 0.1122 (OUTLIER) cc_final: 0.0754 (mm110)
REVERT: C   38 TYR cc_start: 0.9050 (m-80) cc_final: 0.8748 (m-80)
REVERT: C  146 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8322 (mm-40)
REVERT: D   93 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8597 (mtt)
REVERT: D  145 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9105 (tp)
REVERT: D  239 MET cc_start: 0.7791 (ttt) cc_final: 0.7557 (mtt)
REVERT: E  287 GLN cc_start: 0.1516 (OUTLIER) cc_final: 0.0481 (mm110)
  outliers start: 34
  outliers final: 24
  residues processed: 172
  average time/residue: 0.2444
  time to fit residues: 62.2684
Evaluate side-chains
  173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  184 ASN
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  184 ASN
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   chunk 139 optimal weight:    2.9990
   chunk 104 optimal weight:    9.9990
   chunk 102 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 87 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.148826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.117182 restraints weight = 14397.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 0.95
r_work: 0.3013 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12880  Z= 0.142
  Angle     :  0.553   9.331  17545  Z= 0.283
  Chirality :  0.047   0.170   1950
  Planarity :  0.004   0.051   2235
  Dihedral  :  4.780  21.401   1690
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.76 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.22), residues: 1525
  helix:  1.41 (0.23), residues: 540
  sheet:  0.72 (0.26), residues: 470
  loop : -3.00 (0.22), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 177 
 PHE   0.012   0.001   PHE B 247 
 TYR   0.013   0.001   TYR C 245 
 ARG   0.012   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03501 (  575)
  hydrogen bonds       : angle       4.10325 ( 1830)
  covalent geometry    : bond        0.00339 (12880)
  covalent geometry    : angle       0.55326 (17545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6203.51 seconds
wall clock time: 107 minutes 40.84 seconds (6460.84 seconds total)