Starting phenix.real_space_refine
on Tue May 13 22:43:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rk8_19264/05_2025/8rk8_19264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rk8_19264/05_2025/8rk8_19264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rk8_19264/05_2025/8rk8_19264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rk8_19264/05_2025/8rk8_19264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rk8_19264/05_2025/8rk8_19264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rk8_19264/05_2025/8rk8_19264.cif"
  }
  resolution = 3.88
  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=   0.000 sd=   0.002
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      18      5.16       5
     C    7194      2.51       5
     N    1854      2.21       5
     O    2160      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11226
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1871
          Classifications: {'peptide': 252}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 235}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.03, per 1000 atoms: 0.36
  Number of scatterers: 11226
  At special positions: 0
  Unit cell: (150.882, 162.552, 59.1856, 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      18     16.00
     O    2160      8.00
     N    1854      7.00
     C    7194      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=18, symmetry=0
  Number of additional bonds: simple=18, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.95
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2700

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 30 sheets defined
      6.3% alpha, 54.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 84
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 142 through 145
    Processing helix  chain 'B' and resid 76 through 84
    Processing helix  chain 'B' and resid 134 through 136
      No H-bonds generated for 'chain 'B' and resid 134 through 136'
    Processing helix  chain 'B' and resid 142 through 145
    Processing helix  chain 'C' and resid 76 through 84
    Processing helix  chain 'C' and resid 134 through 136
      No H-bonds generated for 'chain 'C' and resid 134 through 136'
    Processing helix  chain 'C' and resid 142 through 145
    Processing helix  chain 'D' and resid 76 through 84
    Processing helix  chain 'D' and resid 134 through 136
      No H-bonds generated for 'chain 'D' and resid 134 through 136'
    Processing helix  chain 'D' and resid 142 through 145
    Processing helix  chain 'E' and resid 76 through 84
    Processing helix  chain 'E' and resid 134 through 136
      No H-bonds generated for 'chain 'E' and resid 134 through 136'
    Processing helix  chain 'E' and resid 142 through 145
    Processing helix  chain 'F' and resid 76 through 84
    Processing helix  chain 'F' and resid 134 through 136
      No H-bonds generated for 'chain 'F' and resid 134 through 136'
    Processing helix  chain 'F' and resid 142 through 145
    Processing sheet with id=1, first strand: chain 'A' and resid 22 through 23
      removed outlier: 3.544A  pdb=" N   VAL A  19 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR A 184 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 185 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS A 207 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER A 231 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ALA A  66 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   GLU A  42 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LYS A  64 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ALA A  40 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ALA A  66 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLN A  38 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL A  68 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   SER A  36 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE A  70 " --> pdb=" O   ALA A  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA A  34 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU A  72 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL A  32 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 27 through 28
      removed outlier: 4.406A  pdb=" N   THR A 184 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 185 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS A 207 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'A' and resid 88 through 91
    Processing sheet with id=4, first strand: chain 'A' and resid 94 through 100
      removed outlier: 5.249A  pdb=" N   SER A  95 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TYR A 169 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   THR A  97 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   TYR A 167 " --> pdb=" O   THR A  97 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLU A 168 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   GLU A 120 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'A' and resid 110 through 112
      removed outlier: 4.876A  pdb=" N   GLU A 148 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 22 through 23
      removed outlier: 3.544A  pdb=" N   VAL B  19 " --> pdb=" O   VAL B  22 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR B 184 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL B 185 " --> pdb=" O   LYS B 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS B 207 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER B 231 " --> pdb=" O   ASP B 211 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ALA B  66 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   GLU B  42 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LYS B  64 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ALA B  40 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ALA B  66 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLN B  38 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL B  68 " --> pdb=" O   SER B  36 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   SER B  36 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE B  70 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA B  34 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU B  72 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B  32 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 27 through 28
      removed outlier: 4.406A  pdb=" N   THR B 184 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL B 185 " --> pdb=" O   LYS B 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS B 207 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'B' and resid 88 through 91
    Processing sheet with id=9, first strand: chain 'B' and resid 94 through 100
      removed outlier: 5.249A  pdb=" N   SER B  95 " --> pdb=" O   TYR B 169 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TYR B 169 " --> pdb=" O   SER B  95 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   THR B  97 " --> pdb=" O   TYR B 167 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   TYR B 167 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   GLU B 168 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   GLU B 120 " --> pdb=" O   GLU B 168 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'B' and resid 110 through 112
      removed outlier: 4.876A  pdb=" N   GLU B 148 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'C' and resid 22 through 23
      removed outlier: 3.544A  pdb=" N   VAL C  19 " --> pdb=" O   VAL C  22 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR C 184 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL C 185 " --> pdb=" O   LYS C 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS C 207 " --> pdb=" O   VAL C 185 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER C 231 " --> pdb=" O   ASP C 211 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ALA C  66 " --> pdb=" O   ILE C 234 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   GLU C  42 " --> pdb=" O   ILE C  62 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LYS C  64 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ALA C  40 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ALA C  66 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLN C  38 " --> pdb=" O   ALA C  66 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL C  68 " --> pdb=" O   SER C  36 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   SER C  36 " --> pdb=" O   VAL C  68 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE C  70 " --> pdb=" O   ALA C  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA C  34 " --> pdb=" O   ILE C  70 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU C  72 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL C  32 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'C' and resid 27 through 28
      removed outlier: 4.406A  pdb=" N   THR C 184 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL C 185 " --> pdb=" O   LYS C 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS C 207 " --> pdb=" O   VAL C 185 " (cutoff:3.500A)
    Processing sheet with id=13, first strand: chain 'C' and resid 88 through 91
    Processing sheet with id=14, first strand: chain 'C' and resid 94 through 100
      removed outlier: 5.250A  pdb=" N   SER C  95 " --> pdb=" O   TYR C 169 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TYR C 169 " --> pdb=" O   SER C  95 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   THR C  97 " --> pdb=" O   TYR C 167 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   TYR C 167 " --> pdb=" O   THR C  97 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   GLU C 168 " --> pdb=" O   GLU C 120 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   GLU C 120 " --> pdb=" O   GLU C 168 " (cutoff:3.500A)
    Processing sheet with id=15, first strand: chain 'C' and resid 110 through 112
      removed outlier: 4.876A  pdb=" N   GLU C 148 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
    Processing sheet with id=16, first strand: chain 'D' and resid 22 through 23
      removed outlier: 3.544A  pdb=" N   VAL D  19 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR D 184 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL D 185 " --> pdb=" O   LYS D 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS D 207 " --> pdb=" O   VAL D 185 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER D 231 " --> pdb=" O   ASP D 211 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ALA D  66 " --> pdb=" O   ILE D 234 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   GLU D  42 " --> pdb=" O   ILE D  62 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LYS D  64 " --> pdb=" O   ALA D  40 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ALA D  40 " --> pdb=" O   LYS D  64 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ALA D  66 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLN D  38 " --> pdb=" O   ALA D  66 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL D  68 " --> pdb=" O   SER D  36 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   SER D  36 " --> pdb=" O   VAL D  68 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE D  70 " --> pdb=" O   ALA D  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA D  34 " --> pdb=" O   ILE D  70 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU D  72 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL D  32 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'D' and resid 27 through 28
      removed outlier: 4.406A  pdb=" N   THR D 184 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL D 185 " --> pdb=" O   LYS D 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS D 207 " --> pdb=" O   VAL D 185 " (cutoff:3.500A)
    Processing sheet with id=18, first strand: chain 'D' and resid 88 through 91
    Processing sheet with id=19, first strand: chain 'D' and resid 94 through 100
      removed outlier: 5.249A  pdb=" N   SER D  95 " --> pdb=" O   TYR D 169 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TYR D 169 " --> pdb=" O   SER D  95 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   THR D  97 " --> pdb=" O   TYR D 167 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   TYR D 167 " --> pdb=" O   THR D  97 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLU D 168 " --> pdb=" O   GLU D 120 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   GLU D 120 " --> pdb=" O   GLU D 168 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'D' and resid 110 through 112
      removed outlier: 4.876A  pdb=" N   GLU D 148 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
    Processing sheet with id=21, first strand: chain 'E' and resid 22 through 23
      removed outlier: 3.544A  pdb=" N   VAL E  19 " --> pdb=" O   VAL E  22 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR E 184 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL E 185 " --> pdb=" O   LYS E 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS E 207 " --> pdb=" O   VAL E 185 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER E 231 " --> pdb=" O   ASP E 211 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ALA E  66 " --> pdb=" O   ILE E 234 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   GLU E  42 " --> pdb=" O   ILE E  62 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LYS E  64 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ALA E  40 " --> pdb=" O   LYS E  64 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ALA E  66 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLN E  38 " --> pdb=" O   ALA E  66 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL E  68 " --> pdb=" O   SER E  36 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   SER E  36 " --> pdb=" O   VAL E  68 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE E  70 " --> pdb=" O   ALA E  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA E  34 " --> pdb=" O   ILE E  70 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU E  72 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL E  32 " --> pdb=" O   LEU E  72 " (cutoff:3.500A)
    Processing sheet with id=22, first strand: chain 'E' and resid 27 through 28
      removed outlier: 4.406A  pdb=" N   THR E 184 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL E 185 " --> pdb=" O   LYS E 207 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   LYS E 207 " --> pdb=" O   VAL E 185 " (cutoff:3.500A)
    Processing sheet with id=23, first strand: chain 'E' and resid 88 through 91
    Processing sheet with id=24, first strand: chain 'E' and resid 94 through 100
      removed outlier: 5.249A  pdb=" N   SER E  95 " --> pdb=" O   TYR E 169 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TYR E 169 " --> pdb=" O   SER E  95 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   THR E  97 " --> pdb=" O   TYR E 167 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   TYR E 167 " --> pdb=" O   THR E  97 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLU E 168 " --> pdb=" O   GLU E 120 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   GLU E 120 " --> pdb=" O   GLU E 168 " (cutoff:3.500A)
    Processing sheet with id=25, first strand: chain 'E' and resid 110 through 112
      removed outlier: 4.876A  pdb=" N   GLU E 148 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
    Processing sheet with id=26, first strand: chain 'F' and resid 22 through 23
      removed outlier: 3.544A  pdb=" N   VAL F  19 " --> pdb=" O   VAL F  22 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR F 184 " --> pdb=" O   ILE F  18 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL F 185 " --> pdb=" O   LYS F 207 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   LYS F 207 " --> pdb=" O   VAL F 185 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER F 231 " --> pdb=" O   ASP F 211 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ALA F  66 " --> pdb=" O   ILE F 234 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   GLU F  42 " --> pdb=" O   ILE F  62 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LYS F  64 " --> pdb=" O   ALA F  40 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ALA F  40 " --> pdb=" O   LYS F  64 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ALA F  66 " --> pdb=" O   GLN F  38 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLN F  38 " --> pdb=" O   ALA F  66 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL F  68 " --> pdb=" O   SER F  36 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   SER F  36 " --> pdb=" O   VAL F  68 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ILE F  70 " --> pdb=" O   ALA F  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA F  34 " --> pdb=" O   ILE F  70 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU F  72 " --> pdb=" O   VAL F  32 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL F  32 " --> pdb=" O   LEU F  72 " (cutoff:3.500A)
    Processing sheet with id=27, first strand: chain 'F' and resid 27 through 28
      removed outlier: 4.406A  pdb=" N   THR F 184 " --> pdb=" O   ILE F  18 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL F 185 " --> pdb=" O   LYS F 207 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   LYS F 207 " --> pdb=" O   VAL F 185 " (cutoff:3.500A)
    Processing sheet with id=28, first strand: chain 'F' and resid 88 through 91
    Processing sheet with id=29, first strand: chain 'F' and resid 94 through 100
      removed outlier: 5.249A  pdb=" N   SER F  95 " --> pdb=" O   TYR F 169 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   TYR F 169 " --> pdb=" O   SER F  95 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   THR F  97 " --> pdb=" O   TYR F 167 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   TYR F 167 " --> pdb=" O   THR F  97 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   GLU F 168 " --> pdb=" O   GLU F 120 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   GLU F 120 " --> pdb=" O   GLU F 168 " (cutoff:3.500A)
    Processing sheet with id=30, first strand: chain 'F' and resid 110 through 112
      removed outlier: 4.876A  pdb=" N   GLU F 148 " --> pdb=" O   ARG F 141 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1260 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: 3.08

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3672
        1.34 -     1.46: 2134
        1.46 -     1.57: 5606
        1.57 -     1.69: 6
        1.69 -     1.80: 36
  Bond restraints: 11454
  Sorted by residual:
  bond pdb=" C   THR C 210 "
       pdb=" N   ASP C 211 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.027 1.36e-02 5.41e+03 3.98e+00
  bond pdb=" C   THR B 210 "
       pdb=" N   ASP B 211 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.027 1.36e-02 5.41e+03 3.96e+00
  bond pdb=" C   THR A 210 "
       pdb=" N   ASP A 211 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.027 1.36e-02 5.41e+03 3.93e+00
  bond pdb=" C   THR D 210 "
       pdb=" N   ASP D 211 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.027 1.36e-02 5.41e+03 3.93e+00
  bond pdb=" C   THR F 210 "
       pdb=" N   ASP F 211 "
    ideal  model  delta    sigma   weight residual
    1.331  1.357 -0.027 1.36e-02 5.41e+03 3.81e+00
  ... (remaining 11449 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 15332
        1.61 -     3.21: 229
        3.21 -     4.82: 63
        4.82 -     6.42: 0
        6.42 -     8.03: 6
  Bond angle restraints: 15630
  Sorted by residual:
  angle pdb=" CA  PRO C 212 "
        pdb=" N   PRO C 212 "
        pdb=" CD  PRO C 212 "
      ideal   model   delta    sigma   weight residual
     112.00  103.97    8.03 1.40e+00 5.10e-01 3.29e+01
  angle pdb=" CA  PRO B 212 "
        pdb=" N   PRO B 212 "
        pdb=" CD  PRO B 212 "
      ideal   model   delta    sigma   weight residual
     112.00  103.99    8.01 1.40e+00 5.10e-01 3.27e+01
  angle pdb=" CA  PRO E 212 "
        pdb=" N   PRO E 212 "
        pdb=" CD  PRO E 212 "
      ideal   model   delta    sigma   weight residual
     112.00  103.99    8.01 1.40e+00 5.10e-01 3.27e+01
  angle pdb=" CA  PRO D 212 "
        pdb=" N   PRO D 212 "
        pdb=" CD  PRO D 212 "
      ideal   model   delta    sigma   weight residual
     112.00  104.00    8.00 1.40e+00 5.10e-01 3.26e+01
  angle pdb=" CA  PRO A 212 "
        pdb=" N   PRO A 212 "
        pdb=" CD  PRO A 212 "
      ideal   model   delta    sigma   weight residual
     112.00  104.00    8.00 1.40e+00 5.10e-01 3.26e+01
  ... (remaining 15625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 6157
       17.95 -    35.90: 521
       35.90 -    53.86: 114
       53.86 -    71.81: 24
       71.81 -    89.76: 12
  Dihedral angle restraints: 6828
    sinusoidal: 2556
      harmonic: 4272
  Sorted by residual:
  dihedral pdb=" CB  GLU C  48 "
           pdb=" CG  GLU C  48 "
           pdb=" CD  GLU C  48 "
           pdb=" OE1 GLU C  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.76  -89.76     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B  48 "
           pdb=" CG  GLU B  48 "
           pdb=" CD  GLU B  48 "
           pdb=" OE1 GLU B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU E  48 "
           pdb=" CG  GLU E  48 "
           pdb=" CD  GLU E  48 "
           pdb=" OE1 GLU E  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 6825 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 950
       0.026 -    0.052: 529
       0.052 -    0.078: 123
       0.078 -    0.104: 99
       0.104 -    0.131: 129
  Chirality restraints: 1830
  Sorted by residual:
  chirality pdb=" CA  ILE F 192 "
            pdb=" N   ILE F 192 "
            pdb=" C   ILE F 192 "
            pdb=" CB  ILE F 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE C 252 "
            pdb=" N   ILE C 252 "
            pdb=" C   ILE C 252 "
            pdb=" CB  ILE C 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  ILE B  18 "
            pdb=" N   ILE B  18 "
            pdb=" C   ILE B  18 "
            pdb=" CB  ILE B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 1827 not shown)

  Planarity restraints: 2028
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 211 "   -0.082 5.00e-02 4.00e+02   1.19e-01 2.28e+01
        pdb=" N   PRO C 212 "    0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO C 212 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO C 212 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 211 "    0.082 5.00e-02 4.00e+02   1.19e-01 2.27e+01
        pdb=" N   PRO E 212 "   -0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO E 212 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO E 212 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 211 "    0.082 5.00e-02 4.00e+02   1.19e-01 2.27e+01
        pdb=" N   PRO A 212 "   -0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO A 212 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A 212 "    0.063 5.00e-02 4.00e+02
  ... (remaining 2025 not shown)

  Histogram of nonbonded interaction distances:
        0.53 -     1.40: 102
        1.40 -     2.28: 210
        2.28 -     3.15: 9210
        3.15 -     4.03: 26374
        4.03 -     4.90: 49316
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 85212
  Sorted by model distance:
  nonbonded pdb=" SD  MET C 177 "
            pdb=" O   GLY D 250 "
     model   vdw
     0.528 3.400
  nonbonded pdb=" SD  MET B 177 "
            pdb=" O   GLY C 250 "
     model   vdw
     0.528 3.400
  nonbonded pdb=" O   GLY A 250 "
            pdb=" SD  MET F 177 "
     model   vdw
     0.528 3.400
  nonbonded pdb=" SD  MET E 177 "
            pdb=" O   GLY F 250 "
     model   vdw
     0.529 3.400
  nonbonded pdb=" SD  MET D 177 "
            pdb=" O   GLY E 250 "
     model   vdw
     0.529 3.400
  ... (remaining 85207 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'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  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:             0.000
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     23.750
  Find NCS groups from input model:        0.370
  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:2.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6438
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      :  0.037   0.954  11472  Z= 3.737
  Angle     :  0.550   8.027  15630  Z= 0.305
  Chirality :  0.047   0.131   1830
  Planarity :  0.008   0.119   2028
  Dihedral  : 14.928  89.759   4128
  Min Nonbonded Distance : 0.528

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.36 (0.22), residues: 1500
  helix:  0.59 (0.79), residues: 54
  sheet:  0.62 (0.19), residues: 732
  loop : -0.09 (0.23), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  28 
 HIS   0.001   0.000   HIS E  46 
 PHE   0.007   0.001   PHE F  60 
 TYR   0.011   0.001   TYR E 169 
 ARG   0.001   0.000   ARG C 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15445 (  360)
  hydrogen bonds       : angle       6.19143 ( 1260)
  covalent geometry    : bond        0.00305 (11454)
  covalent geometry    : angle       0.54999 (15630)
  Misc. bond           : bond        0.94293 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  550 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 550
  time to evaluate  : 1.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7092 (tpp80)
REVERT: B   99 GLU cc_start: 0.6845 (tt0) cc_final: 0.6426 (tm-30)
REVERT: C  182 GLN cc_start: 0.7457 (tt0) cc_final: 0.7013 (tt0)
REVERT: D   47 LYS cc_start: 0.7645 (mttm) cc_final: 0.7309 (pptt)
REVERT: D   71 THR cc_start: 0.8201 (m) cc_final: 0.7769 (m)
REVERT: D  163 PHE cc_start: 0.7261 (m-10) cc_final: 0.6894 (m-10)
REVERT: D  219 ILE cc_start: 0.7973 (mt) cc_final: 0.7691 (mt)
REVERT: E  220 SER cc_start: 0.8253 (m) cc_final: 0.8046 (t)
REVERT: E  223 ASN cc_start: 0.5435 (p0) cc_final: 0.4654 (t0)
REVERT: F  223 ASN cc_start: 0.5367 (p0) cc_final: 0.4371 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 550
  average time/residue: 0.2482
  time to fit residues: 185.0400
Evaluate side-chains
  324 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 324
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0060
   chunk 45 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 136 optimal weight:    9.9990
   overall best weight:    3.2004

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
A  79 ASN
A 136 GLN
A 174 GLN
A 223 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
B 136 GLN
C  38 GLN
C  79 ASN
C 136 GLN
C 182 GLN
D  79 ASN
E  79 ASN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  69 ASN
F  79 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.100335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.088642 restraints weight = 37861.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.090501 restraints weight = 22550.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.091956 restraints weight = 15455.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.5929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.721  11472  Z= 1.627
  Angle     :  1.134  27.544  15630  Z= 0.558
  Chirality :  0.054   0.240   1830
  Planarity :  0.008   0.080   2028
  Dihedral  :  5.511  19.793   1620
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 22.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 16.41 %
    Favored  : 77.52 %
  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:  0.02 (0.21), residues: 1500
  helix:  0.24 (0.70), residues: 54
  sheet:  0.27 (0.20), residues: 660
  loop : -0.12 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP C  26 
 HIS   0.008   0.002   HIS A  46 
 PHE   0.028   0.003   PHE D  60 
 TYR   0.027   0.003   TYR B  85 
 ARG   0.008   0.002   ARG D 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 (  360)
  hydrogen bonds       : angle       5.66981 ( 1260)
  covalent geometry    : bond        0.04684 (11454)
  covalent geometry    : angle       1.13443 (15630)
  Misc. bond           : bond        0.00488 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  441 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 370
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ASP cc_start: 0.8993 (t0) cc_final: 0.8608 (t0)
REVERT: B   58 ARG cc_start: 0.8401 (ttt-90) cc_final: 0.8017 (ttt-90)
REVERT: B   99 GLU cc_start: 0.8157 (tt0) cc_final: 0.7609 (tm-30)
REVERT: B  109 ASP cc_start: 0.7724 (m-30) cc_final: 0.7513 (m-30)
REVERT: B  188 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8453 (tpp80)
REVERT: B  211 ASP cc_start: 0.8977 (t0) cc_final: 0.8621 (t0)
REVERT: B  224 THR cc_start: 0.9017 (p) cc_final: 0.8753 (t)
REVERT: C   69 ASN cc_start: 0.8864 (m-40) cc_final: 0.8663 (m-40)
REVERT: C   91 LYS cc_start: 0.8718 (tptt) cc_final: 0.8338 (tptm)
REVERT: C   99 GLU cc_start: 0.7392 (tt0) cc_final: 0.7113 (tm-30)
REVERT: D   36 SER cc_start: 0.8003 (m) cc_final: 0.7732 (p)
REVERT: D   47 LYS cc_start: 0.9008 (mttm) cc_final: 0.7679 (pptt)
REVERT: E   27 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8199 (ptm-80)
REVERT: E   33 SER cc_start: 0.9368 (t) cc_final: 0.9070 (p)
REVERT: E   84 LEU cc_start: 0.9327 (mt) cc_final: 0.9053 (mp)
REVERT: E  223 ASN cc_start: 0.7182 (p0) cc_final: 0.6662 (t0)
REVERT: F  148 GLU cc_start: 0.6287 (pm20) cc_final: 0.5807 (pm20)
REVERT: F  223 ASN cc_start: 0.7144 (p0) cc_final: 0.6286 (t0)
  outliers start: 71
  outliers final: 40
  residues processed: 401
  average time/residue: 0.2725
  time to fit residues: 144.9607
Evaluate side-chains
  342 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 302
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   31 ASP
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  184 THR
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain E residue   12 GLU
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   60 PHE
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  111 ILE
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   42 GLU
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  230 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 148 optimal weight:    3.9990
   chunk 145 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   chunk 99 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 126 optimal weight:    8.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
A 223 ASN
B  79 ASN
B 182 GLN
C  79 ASN
C 223 ASN
D  53 GLN
D  73 HIS
D 136 GLN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.100848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.088716 restraints weight = 38482.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.090642 restraints weight = 22238.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.092289 restraints weight = 15086.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.6704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.717  11472  Z= 1.476
  Angle     :  1.009  27.161  15630  Z= 0.487
  Chirality :  0.053   0.431   1830
  Planarity :  0.007   0.126   2028
  Dihedral  :  5.139  21.448   1620
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 20.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 18.63 %
    Favored  : 75.13 %
  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:  0.23 (0.21), residues: 1500
  helix: -0.05 (0.65), residues: 54
  sheet:  0.48 (0.20), residues: 684
  loop : -0.03 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  26 
 HIS   0.006   0.001   HIS A  46 
 PHE   0.022   0.002   PHE D  60 
 TYR   0.040   0.002   TYR D 146 
 ARG   0.008   0.001   ARG A 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  360)
  hydrogen bonds       : angle       5.19731 ( 1260)
  covalent geometry    : bond        0.04260 (11454)
  covalent geometry    : angle       1.00918 (15630)
  Misc. bond           : bond        0.00456 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 323
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.8116 (ttt-90) cc_final: 0.7720 (ttp80)
REVERT: A  148 GLU cc_start: 0.6845 (pm20) cc_final: 0.6515 (pm20)
REVERT: A  211 ASP cc_start: 0.8974 (t0) cc_final: 0.8743 (t0)
REVERT: B   43 LYS cc_start: 0.8359 (pttm) cc_final: 0.8003 (ptmt)
REVERT: B   53 GLN cc_start: 0.7782 (mt0) cc_final: 0.7467 (mt0)
REVERT: B   99 GLU cc_start: 0.8228 (tt0) cc_final: 0.7533 (tm-30)
REVERT: B  211 ASP cc_start: 0.8991 (t0) cc_final: 0.8572 (t0)
REVERT: C   45 GLU cc_start: 0.8457 (pm20) cc_final: 0.8227 (pm20)
REVERT: C   53 GLN cc_start: 0.8411 (tt0) cc_final: 0.8107 (tt0)
REVERT: C   69 ASN cc_start: 0.8841 (m-40) cc_final: 0.8588 (m110)
REVERT: C   91 LYS cc_start: 0.8737 (tptt) cc_final: 0.8368 (tptm)
REVERT: C   99 GLU cc_start: 0.7576 (tt0) cc_final: 0.7218 (tm-30)
REVERT: C  112 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.5539 (mtt180)
REVERT: C  211 ASP cc_start: 0.8644 (t0) cc_final: 0.8380 (t0)
REVERT: D   36 SER cc_start: 0.7950 (m) cc_final: 0.7640 (p)
REVERT: D   47 LYS cc_start: 0.9027 (mttm) cc_final: 0.7841 (pptt)
REVERT: E   12 GLU cc_start: 0.7343 (pt0) cc_final: 0.6662 (pt0)
REVERT: E   99 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8121 (tm-30)
REVERT: E  112 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7332 (mtt180)
REVERT: E  223 ASN cc_start: 0.7472 (p0) cc_final: 0.6824 (t0)
REVERT: F   54 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8357 (mmtp)
REVERT: F  148 GLU cc_start: 0.6259 (pm20) cc_final: 0.5653 (pm20)
REVERT: F  223 ASN cc_start: 0.7387 (p0) cc_final: 0.6506 (t0)
REVERT: F  253 ILE cc_start: 0.9052 (mp) cc_final: 0.8795 (mm)
REVERT: F  255 LEU cc_start: 0.9130 (tp) cc_final: 0.8765 (mm)
  outliers start: 73
  outliers final: 47
  residues processed: 354
  average time/residue: 0.2837
  time to fit residues: 132.0295
Evaluate side-chains
  329 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 279
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue  112 ARG
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   45 GLU
Chi-restraints excluded: chain D residue   67 THR
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  177 MET
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   60 PHE
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue  111 ILE
Chi-restraints excluded: chain E residue  112 ARG
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   42 GLU
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   69 ASN
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  224 THR
Chi-restraints excluded: chain F residue  230 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 86 optimal weight:   20.0000
   chunk 51 optimal weight:    3.9990
   chunk 148 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 140 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 112 optimal weight:    0.5980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 223 ASN
E  53 GLN
E  79 ASN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.099582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.087509 restraints weight = 37667.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.089345 restraints weight = 22242.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.090834 restraints weight = 15451.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.7265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.717  11472  Z= 1.475
  Angle     :  0.987  27.621  15630  Z= 0.473
  Chirality :  0.051   0.243   1830
  Planarity :  0.008   0.164   2028
  Dihedral  :  5.205  32.394   1620
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 19.60
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.00 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 20.77 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.20 (0.21), residues: 1500
  helix: -0.11 (0.66), residues: 54
  sheet:  0.46 (0.21), residues: 582
  loop :  0.01 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  26 
 HIS   0.008   0.001   HIS A  46 
 PHE   0.019   0.002   PHE D  60 
 TYR   0.020   0.002   TYR C 146 
 ARG   0.010   0.001   ARG F 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03929 (  360)
  hydrogen bonds       : angle       4.93369 ( 1260)
  covalent geometry    : bond        0.04258 (11454)
  covalent geometry    : angle       0.98678 (15630)
  Misc. bond           : bond        0.00554 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 309
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8089 (mttt)
REVERT: A   58 ARG cc_start: 0.8214 (ttt-90) cc_final: 0.7831 (ttp80)
REVERT: A   78 ASP cc_start: 0.8125 (t70) cc_final: 0.7741 (t70)
REVERT: A  148 GLU cc_start: 0.6898 (pm20) cc_final: 0.6575 (pm20)
REVERT: A  211 ASP cc_start: 0.8964 (t0) cc_final: 0.8725 (t0)
REVERT: A  246 LEU cc_start: 0.8271 (pt) cc_final: 0.7925 (pp)
REVERT: B   43 LYS cc_start: 0.8293 (pttm) cc_final: 0.8090 (ptmt)
REVERT: B   58 ARG cc_start: 0.8447 (tpt90) cc_final: 0.8102 (tpt-90)
REVERT: B   99 GLU cc_start: 0.8135 (tt0) cc_final: 0.7553 (tm-30)
REVERT: B  211 ASP cc_start: 0.9022 (t0) cc_final: 0.8731 (t0)
REVERT: C   45 GLU cc_start: 0.8534 (pm20) cc_final: 0.8171 (pm20)
REVERT: C   58 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8406 (tpt90)
REVERT: C   60 PHE cc_start: 0.8301 (p90) cc_final: 0.8033 (p90)
REVERT: C   99 GLU cc_start: 0.7532 (tt0) cc_final: 0.7194 (tm-30)
REVERT: D   36 SER cc_start: 0.8049 (m) cc_final: 0.7721 (p)
REVERT: D   48 GLU cc_start: 0.6782 (pp20) cc_final: 0.6573 (tp30)
REVERT: D   58 ARG cc_start: 0.8467 (mmm160) cc_final: 0.8055 (tpt-90)
REVERT: E   53 GLN cc_start: 0.8678 (mt0) cc_final: 0.8370 (mt0)
REVERT: E  112 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6909 (ptp-110)
REVERT: E  141 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7993 (mtm-85)
REVERT: E  223 ASN cc_start: 0.7728 (p0) cc_final: 0.7074 (t0)
REVERT: F   54 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8303 (mmtt)
REVERT: F  148 GLU cc_start: 0.6495 (pm20) cc_final: 0.5808 (pm20)
REVERT: F  223 ASN cc_start: 0.7566 (p0) cc_final: 0.6665 (t0)
REVERT: F  255 LEU cc_start: 0.9151 (tp) cc_final: 0.8729 (mm)
  outliers start: 78
  outliers final: 51
  residues processed: 350
  average time/residue: 0.2832
  time to fit residues: 130.6519
Evaluate side-chains
  333 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 279
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   67 THR
Chi-restraints excluded: chain D residue   79 ASN
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   60 PHE
Chi-restraints excluded: chain E residue  112 ARG
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   42 GLU
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  215 GLU
Chi-restraints excluded: chain F residue  235 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 87 optimal weight:    0.6980
   chunk 101 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 119 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
A 223 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
C  38 GLN
C  79 ASN
D 223 ASN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.100562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.088393 restraints weight = 37308.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.090170 restraints weight = 21880.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.091571 restraints weight = 15225.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.7719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.716  11472  Z= 1.474
  Angle     :  0.978  28.056  15630  Z= 0.471
  Chirality :  0.052   0.366   1830
  Planarity :  0.008   0.168   2028
  Dihedral  :  5.164  35.028   1620
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 22.22 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.26 (0.21), residues: 1500
  helix:  0.14 (0.66), residues: 54
  sheet:  0.66 (0.21), residues: 600
  loop : -0.11 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  26 
 HIS   0.007   0.001   HIS A  46 
 PHE   0.017   0.001   PHE D  60 
 TYR   0.023   0.001   TYR D 146 
 ARG   0.016   0.001   ARG F 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  360)
  hydrogen bonds       : angle       4.81612 ( 1260)
  covalent geometry    : bond        0.04255 (11454)
  covalent geometry    : angle       0.97761 (15630)
  Misc. bond           : bond        0.00561 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 284
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7757 (mttt)
REVERT: A   58 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7669 (tmm-80)
REVERT: A  211 ASP cc_start: 0.8913 (t0) cc_final: 0.8665 (t0)
REVERT: B   58 ARG cc_start: 0.8430 (tpt90) cc_final: 0.8182 (tpt-90)
REVERT: B   99 GLU cc_start: 0.8153 (tt0) cc_final: 0.7607 (tm-30)
REVERT: C   45 GLU cc_start: 0.8586 (pm20) cc_final: 0.8192 (pm20)
REVERT: C   58 ARG cc_start: 0.8684 (tpt90) cc_final: 0.8377 (tpt90)
REVERT: C   60 PHE cc_start: 0.8340 (p90) cc_final: 0.8085 (p90)
REVERT: C  177 MET cc_start: 0.8030 (mpp) cc_final: 0.7800 (mpp)
REVERT: D   36 SER cc_start: 0.8075 (m) cc_final: 0.7814 (p)
REVERT: E  112 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6862 (ptp-110)
REVERT: E  148 GLU cc_start: 0.6737 (pm20) cc_final: 0.5965 (pm20)
REVERT: E  223 ASN cc_start: 0.7803 (p0) cc_final: 0.7161 (t0)
REVERT: F   54 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8276 (mmtt)
REVERT: F  223 ASN cc_start: 0.7681 (p0) cc_final: 0.6703 (t0)
REVERT: F  224 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8530 (t)
REVERT: F  255 LEU cc_start: 0.9094 (tp) cc_final: 0.8704 (mm)
  outliers start: 69
  outliers final: 45
  residues processed: 323
  average time/residue: 0.2653
  time to fit residues: 114.0070
Evaluate side-chains
  320 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 271
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   79 ASN
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   60 PHE
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  112 ARG
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  215 GLU
Chi-restraints excluded: chain F residue  224 THR
Chi-restraints excluded: chain F residue  235 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 118 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 145 optimal weight:    5.9990
   chunk 110 optimal weight:   20.0000
   chunk 78 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
C 254 GLN
D  53 GLN
D 223 ASN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  79 ASN
F 136 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.092725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.080821 restraints weight = 38972.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.082464 restraints weight = 22727.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.083739 restraints weight = 15780.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.8912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.728  11472  Z= 1.492
  Angle     :  1.097  27.842  15630  Z= 0.532
  Chirality :  0.053   0.292   1830
  Planarity :  0.007   0.111   2028
  Dihedral  :  6.073  42.325   1620
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 21.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 23.50 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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:  0.04 (0.21), residues: 1500
  helix:  0.02 (0.62), residues: 54
  sheet:  0.59 (0.21), residues: 660
  loop : -0.41 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP E  26 
 HIS   0.040   0.004   HIS A  46 
 PHE   0.014   0.002   PHE F 249 
 TYR   0.018   0.002   TYR A  50 
 ARG   0.010   0.001   ARG D 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04729 (  360)
  hydrogen bonds       : angle       5.12622 ( 1260)
  covalent geometry    : bond        0.04285 (11454)
  covalent geometry    : angle       1.09675 (15630)
  Misc. bond           : bond        0.00510 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 285
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8412 (mttt)
REVERT: A   58 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.8095 (ttp80)
REVERT: A   79 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8577 (m-40)
REVERT: A  211 ASP cc_start: 0.8887 (t0) cc_final: 0.8630 (t0)
REVERT: B   58 ARG cc_start: 0.8496 (tpt90) cc_final: 0.8279 (tpt-90)
REVERT: B   99 GLU cc_start: 0.8431 (tt0) cc_final: 0.7961 (tm-30)
REVERT: B  211 ASP cc_start: 0.8583 (t0) cc_final: 0.8324 (t0)
REVERT: C   45 GLU cc_start: 0.8675 (pm20) cc_final: 0.8201 (pm20)
REVERT: C   46 HIS cc_start: 0.7883 (t70) cc_final: 0.7673 (t70)
REVERT: C   53 GLN cc_start: 0.8499 (tt0) cc_final: 0.8093 (tt0)
REVERT: C   58 ARG cc_start: 0.8617 (tpt90) cc_final: 0.8341 (tpt-90)
REVERT: C   72 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8722 (pp)
REVERT: C  149 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8132 (m)
REVERT: C  211 ASP cc_start: 0.8862 (t70) cc_final: 0.8285 (t0)
REVERT: C  223 ASN cc_start: 0.4845 (t0) cc_final: 0.4524 (t0)
REVERT: C  229 GLN cc_start: 0.8567 (tt0) cc_final: 0.8351 (tt0)
REVERT: D   58 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.6500 (mmm160)
REVERT: D   60 PHE cc_start: 0.8527 (p90) cc_final: 0.8285 (p90)
REVERT: E  115 ASN cc_start: 0.8552 (m110) cc_final: 0.8262 (m-40)
REVERT: E  148 GLU cc_start: 0.6860 (pm20) cc_final: 0.6362 (pm20)
REVERT: E  192 ILE cc_start: 0.9295 (mm) cc_final: 0.9052 (tp)
REVERT: F   48 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7397 (tp30)
REVERT: F   54 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8139 (mmtt)
REVERT: F  115 ASN cc_start: 0.8409 (t0) cc_final: 0.8204 (t0)
REVERT: F  223 ASN cc_start: 0.7726 (p0) cc_final: 0.6657 (t0)
REVERT: F  224 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8684 (t)
REVERT: F  255 LEU cc_start: 0.9317 (tp) cc_final: 0.9059 (mm)
  outliers start: 83
  outliers final: 51
  residues processed: 334
  average time/residue: 0.2851
  time to fit residues: 125.9091
Evaluate side-chains
  312 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 254
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   60 PHE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  112 ARG
Chi-restraints excluded: chain B residue  190 LYS
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue   72 LEU
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   50 TYR
Chi-restraints excluded: chain D residue   58 ARG
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   54 LYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   60 PHE
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   60 PHE
Chi-restraints excluded: chain F residue   65 THR
Chi-restraints excluded: chain F residue  215 GLU
Chi-restraints excluded: chain F residue  224 THR
Chi-restraints excluded: chain F residue  235 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 92 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 142 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
A 223 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.088815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.076869 restraints weight = 40055.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.078562 restraints weight = 22976.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.079851 restraints weight = 15601.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.9502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.729  11472  Z= 1.500
  Angle     :  1.163  28.179  15630  Z= 0.560
  Chirality :  0.053   0.328   1830
  Planarity :  0.008   0.168   2028
  Dihedral  :  6.341  51.089   1620
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 23.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 24.02 %
    Favored  : 69.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -0.33 (0.21), residues: 1500
  helix: -0.27 (0.61), residues: 54
  sheet:  0.48 (0.20), residues: 672
  loop : -0.83 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  26 
 HIS   0.007   0.001   HIS F  46 
 PHE   0.016   0.002   PHE F 163 
 TYR   0.020   0.002   TYR B  50 
 ARG   0.011   0.001   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04865 (  360)
  hydrogen bonds       : angle       5.29975 ( 1260)
  covalent geometry    : bond        0.04298 (11454)
  covalent geometry    : angle       1.16264 (15630)
  Misc. bond           : bond        0.00685 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 248
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8105 (mttt)
REVERT: A   58 ARG cc_start: 0.8510 (ttt-90) cc_final: 0.8066 (ttp80)
REVERT: A   79 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8873 (m-40)
REVERT: A  211 ASP cc_start: 0.8890 (t0) cc_final: 0.8600 (t0)
REVERT: B   85 TYR cc_start: 0.8693 (m-80) cc_final: 0.8420 (m-80)
REVERT: C   43 LYS cc_start: 0.8805 (pttm) cc_final: 0.8361 (ptpt)
REVERT: C   45 GLU cc_start: 0.8675 (pm20) cc_final: 0.8346 (pm20)
REVERT: C   46 HIS cc_start: 0.8000 (t70) cc_final: 0.7768 (t70)
REVERT: C   58 ARG cc_start: 0.8658 (tpt90) cc_final: 0.8423 (tpt-90)
REVERT: C   85 TYR cc_start: 0.8942 (m-80) cc_final: 0.8613 (m-80)
REVERT: C   91 LYS cc_start: 0.8664 (tptt) cc_final: 0.8424 (ttpt)
REVERT: C  211 ASP cc_start: 0.8962 (t70) cc_final: 0.8537 (t0)
REVERT: D   53 GLN cc_start: 0.8639 (tt0) cc_final: 0.7814 (pm20)
REVERT: D   58 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.6620 (mtm110)
REVERT: E  115 ASN cc_start: 0.8666 (m110) cc_final: 0.8356 (m-40)
REVERT: E  148 GLU cc_start: 0.6687 (pm20) cc_final: 0.6094 (pm20)
REVERT: F   54 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8365 (mmtt)
REVERT: F   99 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8389 (tm-30)
  outliers start: 78
  outliers final: 61
  residues processed: 294
  average time/residue: 0.2906
  time to fit residues: 112.7739
Evaluate side-chains
  298 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 233
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   60 PHE
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   60 PHE
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  190 LYS
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   50 TYR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   58 ARG
Chi-restraints excluded: chain D residue   67 THR
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   54 LYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   60 PHE
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   68 VAL
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  228 MET
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   60 PHE
Chi-restraints excluded: chain F residue   65 THR
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  215 GLU
Chi-restraints excluded: chain F residue  235 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 106 optimal weight:    8.9990
   chunk 89 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 142 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
B 254 GLN
C  38 GLN
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.091858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.080094 restraints weight = 38736.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.081832 restraints weight = 22341.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.082995 restraints weight = 15185.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.9700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.719  11472  Z= 1.480
  Angle     :  1.098  28.482  15630  Z= 0.523
  Chirality :  0.051   0.202   1830
  Planarity :  0.007   0.101   2028
  Dihedral  :  5.934  46.780   1620
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 26.32 %
    Favored  : 67.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.27 (0.21), residues: 1500
  helix:  0.10 (0.64), residues: 54
  sheet:  0.46 (0.20), residues: 672
  loop : -0.74 (0.21), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  26 
 HIS   0.015   0.002   HIS A  46 
 PHE   0.018   0.001   PHE D  60 
 TYR   0.017   0.002   TYR B  50 
 ARG   0.009   0.001   ARG E 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04420 (  360)
  hydrogen bonds       : angle       5.07049 ( 1260)
  covalent geometry    : bond        0.04264 (11454)
  covalent geometry    : angle       1.09799 (15630)
  Misc. bond           : bond        0.00661 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 248
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8242 (mttt)
REVERT: A   79 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8841 (m-40)
REVERT: A  211 ASP cc_start: 0.8881 (t0) cc_final: 0.8581 (t0)
REVERT: B   85 TYR cc_start: 0.8605 (m-80) cc_final: 0.8382 (m-80)
REVERT: B  211 ASP cc_start: 0.8597 (t0) cc_final: 0.8391 (t0)
REVERT: C   43 LYS cc_start: 0.8637 (pttm) cc_final: 0.8163 (ptpt)
REVERT: C   45 GLU cc_start: 0.8591 (pm20) cc_final: 0.8230 (pm20)
REVERT: C   46 HIS cc_start: 0.7892 (t70) cc_final: 0.7644 (t70)
REVERT: C   91 LYS cc_start: 0.8661 (tptt) cc_final: 0.8407 (ttpt)
REVERT: C  211 ASP cc_start: 0.8865 (t70) cc_final: 0.8470 (t0)
REVERT: D   53 GLN cc_start: 0.8619 (tt0) cc_final: 0.8018 (pm20)
REVERT: E  115 ASN cc_start: 0.8690 (m110) cc_final: 0.8396 (m-40)
REVERT: E  192 ILE cc_start: 0.9274 (mm) cc_final: 0.9007 (tp)
REVERT: F   54 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8163 (mmtt)
REVERT: F   99 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8384 (tm-30)
  outliers start: 71
  outliers final: 60
  residues processed: 290
  average time/residue: 0.2917
  time to fit residues: 111.3613
Evaluate side-chains
  291 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 228
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  190 LYS
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  190 LYS
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   50 TYR
Chi-restraints excluded: chain D residue   67 THR
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain E residue   37 ILE
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   54 LYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   60 PHE
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   68 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain E residue  254 GLN
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   79 ASN
Chi-restraints excluded: chain F residue   80 LEU
Chi-restraints excluded: chain F residue  215 GLU
Chi-restraints excluded: chain F residue  235 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 125 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 142 optimal weight:    5.9990
   chunk 145 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 130 optimal weight:    5.9990
   chunk 141 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0000
   chunk 5 optimal weight:    0.0060
   chunk 148 optimal weight:    0.5980
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.6602

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 161 GLN
E 254 GLN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.095382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.083261 restraints weight = 38955.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.085105 restraints weight = 22349.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.086535 restraints weight = 15210.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.9778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.715  11472  Z= 1.475
  Angle     :  1.066  27.880  15630  Z= 0.509
  Chirality :  0.051   0.204   1830
  Planarity :  0.006   0.088   2028
  Dihedral  :  5.636  46.672   1620
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 18.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 28.46 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -0.11 (0.21), residues: 1500
  helix:  0.34 (0.65), residues: 54
  sheet:  0.79 (0.22), residues: 576
  loop : -0.71 (0.20), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  26 
 HIS   0.027   0.002   HIS A  46 
 PHE   0.021   0.001   PHE C  60 
 TYR   0.018   0.001   TYR F  85 
 ARG   0.007   0.001   ARG F  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  360)
  hydrogen bonds       : angle       4.90457 ( 1260)
  covalent geometry    : bond        0.04254 (11454)
  covalent geometry    : angle       1.06605 (15630)
  Misc. bond           : bond        0.00687 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 281
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8531 (mttt)
REVERT: A  141 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7777 (ttm170)
REVERT: A  211 ASP cc_start: 0.8821 (t0) cc_final: 0.8478 (t0)
REVERT: B   99 GLU cc_start: 0.8370 (tt0) cc_final: 0.8058 (tm-30)
REVERT: B  101 LEU cc_start: 0.8922 (mt) cc_final: 0.8394 (mt)
REVERT: C   42 GLU cc_start: 0.8463 (pm20) cc_final: 0.8225 (pm20)
REVERT: C   43 LYS cc_start: 0.8594 (pttm) cc_final: 0.8127 (ptpt)
REVERT: C   45 GLU cc_start: 0.8508 (pm20) cc_final: 0.7920 (pm20)
REVERT: C   49 SER cc_start: 0.7748 (t) cc_final: 0.7435 (p)
REVERT: C  215 GLU cc_start: 0.8289 (pt0) cc_final: 0.7518 (tt0)
REVERT: D   53 GLN cc_start: 0.8557 (tt0) cc_final: 0.8090 (pm20)
REVERT: D   58 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8527 (tpt-90)
REVERT: D  192 ILE cc_start: 0.9218 (mt) cc_final: 0.9006 (tp)
REVERT: E  115 ASN cc_start: 0.8583 (m110) cc_final: 0.8308 (m-40)
REVERT: E  192 ILE cc_start: 0.9105 (mm) cc_final: 0.8818 (tp)
REVERT: F   91 LYS cc_start: 0.8261 (mmmt) cc_final: 0.8008 (mtmt)
REVERT: F   99 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: F  146 TYR cc_start: 0.7602 (m-80) cc_final: 0.7105 (m-80)
REVERT: F  251 ARG cc_start: 0.8880 (ttp-170) cc_final: 0.8548 (ptt-90)
  outliers start: 51
  outliers final: 39
  residues processed: 311
  average time/residue: 0.3099
  time to fit residues: 125.0232
Evaluate side-chains
  286 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 246
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  190 LYS
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  190 LYS
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  221 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  245 ASP
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   54 LYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue  215 GLU
Chi-restraints excluded: chain F residue  235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 14 optimal weight:   50.0000
   chunk 133 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 134 optimal weight:    6.9990
   chunk 135 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    4.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
A  53 GLN
A  79 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
E 254 GLN
** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.091384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.079940 restraints weight = 39625.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.081670 restraints weight = 22854.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.082964 restraints weight = 15531.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          1.0006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.722  11472  Z= 1.489
  Angle     :  1.162  28.374  15630  Z= 0.556
  Chirality :  0.052   0.194   1830
  Planarity :  0.007   0.094   2028
  Dihedral  :  6.084  43.588   1620
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 22.34
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.20 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 28.80 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -0.29 (0.21), residues: 1500
  helix:  0.28 (0.65), residues: 54
  sheet:  0.43 (0.20), residues: 660
  loop : -0.74 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  26 
 HIS   0.022   0.002   HIS A  46 
 PHE   0.015   0.002   PHE F 163 
 TYR   0.017   0.002   TYR E  85 
 ARG   0.009   0.002   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04550 (  360)
  hydrogen bonds       : angle       5.17111 ( 1260)
  covalent geometry    : bond        0.04278 (11454)
  covalent geometry    : angle       1.16179 (15630)
  Misc. bond           : bond        0.00671 (   18)

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 246
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 SER cc_start: 0.7868 (t) cc_final: 0.7489 (p)
REVERT: A   54 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8386 (mttt)
REVERT: A  141 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7993 (ttm170)
REVERT: A  211 ASP cc_start: 0.8873 (t0) cc_final: 0.8560 (t0)
REVERT: C   43 LYS cc_start: 0.8567 (pttm) cc_final: 0.8260 (ptpt)
REVERT: C   45 GLU cc_start: 0.8533 (pm20) cc_final: 0.8190 (pm20)
REVERT: C   85 TYR cc_start: 0.8756 (m-80) cc_final: 0.8230 (m-80)
REVERT: E  115 ASN cc_start: 0.8665 (m110) cc_final: 0.8288 (m110)
REVERT: E  192 ILE cc_start: 0.9300 (mm) cc_final: 0.9056 (tp)
REVERT: F   91 LYS cc_start: 0.8299 (mmmt) cc_final: 0.8068 (mtmt)
REVERT: F  251 ARG cc_start: 0.8957 (ttp-170) cc_final: 0.8699 (ptt-90)
  outliers start: 50
  outliers final: 41
  residues processed: 279
  average time/residue: 0.3153
  time to fit residues: 113.2853
Evaluate side-chains
  269 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 227
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  190 LYS
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  190 LYS
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain D residue  111 ILE
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   46 HIS
Chi-restraints excluded: chain E residue   54 LYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain E residue  254 GLN
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue  215 GLU
Chi-restraints excluded: chain F residue  235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 117 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0470
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 87 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   overall best weight:    2.4086

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.092276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080572 restraints weight = 38579.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.082441 restraints weight = 21989.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.083772 restraints weight = 14776.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          1.0147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.043   1.717  11472  Z= 1.478
  Angle     :  1.154  28.514  15630  Z= 0.553
  Chirality :  0.053   0.210   1830
  Planarity :  0.007   0.093   2028
  Dihedral  :  6.196  47.898   1620
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 29.66 %
    Favored  : 65.90 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -0.23 (0.21), residues: 1500
  helix:  0.72 (0.69), residues: 54
  sheet:  0.42 (0.20), residues: 672
  loop : -0.70 (0.22), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  26 
 HIS   0.029   0.002   HIS A  46 
 PHE   0.015   0.001   PHE F 163 
 TYR   0.018   0.002   TYR E  85 
 ARG   0.011   0.002   ARG A  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04336 (  360)
  hydrogen bonds       : angle       5.15983 ( 1260)
  covalent geometry    : bond        0.04260 (11454)
  covalent geometry    : angle       1.15367 (15630)
  Misc. bond           : bond        0.00743 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3832.81 seconds
wall clock time: 68 minutes 1.12 seconds (4081.12 seconds total)