Starting phenix.real_space_refine
on Fri Jan 17 17:02:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rk8_19264/01_2025/8rk8_19264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rk8_19264/01_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_19264/01_2025/8rk8_19264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rk8_19264/01_2025/8rk8_19264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rk8_19264/01_2025/8rk8_19264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rk8_19264/01_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-5571/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: 4.31, per 1000 atoms: 0.38
  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: 3.30
  Conformation dependent library (CDL) restraints added in 1.6 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: 1.62
  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: 3.32

  Time building geometry restraints manager: 3.65 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: 0.10
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:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     25.280
  Find NCS groups from input model:        0.400
  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:             0.010
  Load rotamer database and sin/cos tables:2.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.720
-------------------------------------------------------------------------------
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      :  0.003   0.084  11454  Z= 0.219
  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 

*********************** 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  : 1.191 
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: 0.2706
  time to fit residues: 201.5210
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  : 1.262 
-------------------------------------------------------------------------------
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:    4.9990
   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:    2.8004

-------------------------------------------------------------------------------
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 174 GLN
A 223 ASN
B  79 ASN
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: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.101547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.089861 restraints weight = 37682.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.091741 restraints weight = 22415.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.093143 restraints weight = 15470.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.718  11454  Z= 3.479
  Angle     :  1.107  26.186  15630  Z= 0.546
  Chirality :  0.054   0.242   1830
  Planarity :  0.008   0.079   2028
  Dihedral  :  5.328  21.209   1620
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 23.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 16.07 %
    Favored  : 77.95 %
  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:  0.05 (0.21), residues: 1500
  helix:  0.27 (0.70), residues: 54
  sheet:  0.27 (0.20), residues: 660
  loop : -0.08 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP F  26 
 HIS   0.008   0.002   HIS A  46 
 PHE   0.030   0.003   PHE D  60 
 TYR   0.026   0.003   TYR D  50 
 ARG   0.009   0.001   ARG F  27 

*********************** 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
  430 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 360
  time to evaluate  : 1.443 
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: A  211 ASP cc_start: 0.8995 (t0) cc_final: 0.8610 (t0)
REVERT: B   58 ARG cc_start: 0.8416 (ttt-90) cc_final: 0.8119 (ttt-90)
REVERT: B   99 GLU cc_start: 0.8054 (tt0) cc_final: 0.7567 (tm-30)
REVERT: B  211 ASP cc_start: 0.8931 (t0) cc_final: 0.8576 (t0)
REVERT: C   58 ARG cc_start: 0.8914 (tpt90) cc_final: 0.8662 (tpt90)
REVERT: C   69 ASN cc_start: 0.8787 (m-40) cc_final: 0.8555 (m-40)
REVERT: C   91 LYS cc_start: 0.8684 (tptt) cc_final: 0.8308 (tptm)
REVERT: C   99 GLU cc_start: 0.7301 (tt0) cc_final: 0.6973 (tm-30)
REVERT: C  163 PHE cc_start: 0.7858 (m-80) cc_final: 0.7620 (m-80)
REVERT: D    6 TYR cc_start: 0.7912 (m-80) cc_final: 0.7700 (m-80)
REVERT: D   36 SER cc_start: 0.7820 (m) cc_final: 0.7581 (p)
REVERT: D   43 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8362 (ttmm)
REVERT: D   47 LYS cc_start: 0.8954 (mttm) cc_final: 0.7573 (pptt)
REVERT: D   53 GLN cc_start: 0.8687 (mt0) cc_final: 0.8465 (tt0)
REVERT: D  204 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7379 (tm-30)
REVERT: E   33 SER cc_start: 0.9349 (t) cc_final: 0.8929 (p)
REVERT: E  223 ASN cc_start: 0.7020 (p0) cc_final: 0.6525 (t0)
REVERT: F  148 GLU cc_start: 0.6215 (pm20) cc_final: 0.5760 (pm20)
REVERT: F  223 ASN cc_start: 0.7091 (p0) cc_final: 0.6215 (t0)
  outliers start: 70
  outliers final: 37
  residues processed: 390
  average time/residue: 0.2807
  time to fit residues: 147.0687
Evaluate side-chains
  331 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 294
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
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  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   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:    6.9990
   chunk 148 optimal weight:    0.9980
   chunk 145 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 99 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0470
   chunk 101 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 126 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.6082

-------------------------------------------------------------------------------
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 182 GLN
** C  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 223 ASN
D  73 HIS
D 136 GLN
D 223 ASN
** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.101499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.089657 restraints weight = 38749.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.091643 restraints weight = 22418.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.092839 restraints weight = 15274.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.6407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.720  11454  Z= 3.465
  Angle     :  1.021  27.646  15630  Z= 0.492
  Chirality :  0.051   0.224   1830
  Planarity :  0.007   0.118   2028
  Dihedral  :  5.055  21.950   1620
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 21.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 18.12 %
    Favored  : 75.98 %
  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:  0.28 (0.22), residues: 1500
  helix: -0.28 (0.67), residues: 54
  sheet:  0.52 (0.20), residues: 684
  loop :  0.03 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  26 
 HIS   0.011   0.002   HIS A  46 
 PHE   0.022   0.002   PHE D  60 
 TYR   0.019   0.002   TYR D  50 
 ARG   0.013   0.001   ARG A 112 

*********************** 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: 69
    poor density    : 327
  time to evaluate  : 1.409 
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: 0.8081 (ttt-90) cc_final: 0.7710 (tmm160)
REVERT: A  204 GLU cc_start: 0.7223 (tp30) cc_final: 0.6898 (mm-30)
REVERT: A  211 ASP cc_start: 0.8990 (t0) cc_final: 0.8769 (t0)
REVERT: B   43 LYS cc_start: 0.8386 (pttm) cc_final: 0.8056 (ptmt)
REVERT: B   53 GLN cc_start: 0.7671 (mt0) cc_final: 0.7342 (mt0)
REVERT: B   58 ARG cc_start: 0.8389 (ttt-90) cc_final: 0.8109 (tpt90)
REVERT: B   99 GLU cc_start: 0.8106 (tt0) cc_final: 0.7513 (tm-30)
REVERT: B  211 ASP cc_start: 0.8950 (t0) cc_final: 0.8711 (t0)
REVERT: C   45 GLU cc_start: 0.8473 (pm20) cc_final: 0.8147 (pm20)
REVERT: C   58 ARG cc_start: 0.8865 (tpt90) cc_final: 0.8658 (tpt90)
REVERT: C   69 ASN cc_start: 0.8834 (m-40) cc_final: 0.8632 (m110)
REVERT: C   91 LYS cc_start: 0.8709 (tptt) cc_final: 0.8341 (tptm)
REVERT: C   99 GLU cc_start: 0.7424 (tt0) cc_final: 0.7069 (tm-30)
REVERT: C  112 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5282 (mtt180)
REVERT: C  206 TYR cc_start: 0.8701 (m-80) cc_final: 0.8338 (m-80)
REVERT: D   36 SER cc_start: 0.7721 (m) cc_final: 0.7518 (p)
REVERT: D   47 LYS cc_start: 0.9012 (mttm) cc_final: 0.7826 (pptt)
REVERT: D   53 GLN cc_start: 0.8808 (mt0) cc_final: 0.8487 (tt0)
REVERT: E   99 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8059 (tm-30)
REVERT: E  141 ARG cc_start: 0.8234 (ttm170) cc_final: 0.8012 (mtm110)
REVERT: E  223 ASN cc_start: 0.7535 (p0) cc_final: 0.6942 (t0)
REVERT: F  148 GLU cc_start: 0.6306 (pm20) cc_final: 0.5656 (pm20)
REVERT: F  223 ASN cc_start: 0.7343 (p0) cc_final: 0.6455 (t0)
REVERT: F  253 ILE cc_start: 0.9007 (mp) cc_final: 0.8728 (mm)
REVERT: F  255 LEU cc_start: 0.9098 (tp) cc_final: 0.8737 (mm)
  outliers start: 69
  outliers final: 38
  residues processed: 358
  average time/residue: 0.3045
  time to fit residues: 143.6393
Evaluate side-chains
  324 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 285
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   31 ASP
Chi-restraints excluded: chain D residue   45 GLU
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  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 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  149 VAL
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain F residue   22 VAL
Chi-restraints excluded: chain F residue   42 GLU
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:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 148 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 140 optimal weight:    0.9990
   chunk 109 optimal weight:    0.4980
   chunk 2 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0570
   chunk 128 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.5104

-------------------------------------------------------------------------------
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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  79 ASN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.100496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.088363 restraints weight = 38304.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.090215 restraints weight = 22253.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.091717 restraints weight = 15222.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.7036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.715  11454  Z= 3.461
  Angle     :  1.020  28.492  15630  Z= 0.484
  Chirality :  0.050   0.202   1830
  Planarity :  0.008   0.145   2028
  Dihedral  :  5.100  34.712   1620
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 19.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.27 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 21.20 %
    Favored  : 72.99 %
  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:  0.18 (0.21), residues: 1500
  helix:  0.26 (0.67), residues: 54
  sheet:  0.49 (0.20), residues: 642
  loop : -0.10 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C  26 
 HIS   0.006   0.001   HIS A  46 
 PHE   0.019   0.002   PHE D  60 
 TYR   0.021   0.002   TYR B 146 
 ARG   0.022   0.001   ARG B 112 

*********************** 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
  382 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 314
  time to evaluate  : 1.367 
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: 0.8425 (OUTLIER) cc_final: 0.7992 (mttt)
REVERT: A   58 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.7907 (tmm160)
REVERT: A  211 ASP cc_start: 0.8920 (t0) cc_final: 0.8688 (t0)
REVERT: A  246 LEU cc_start: 0.8387 (pt) cc_final: 0.8169 (pt)
REVERT: B   85 TYR cc_start: 0.8032 (m-80) cc_final: 0.7831 (m-80)
REVERT: B   99 GLU cc_start: 0.8117 (tt0) cc_final: 0.7596 (tm-30)
REVERT: B  228 MET cc_start: 0.8205 (mtt) cc_final: 0.7903 (mtt)
REVERT: C   45 GLU cc_start: 0.8542 (pm20) cc_final: 0.8173 (pm20)
REVERT: C   58 ARG cc_start: 0.8841 (tpt90) cc_final: 0.8612 (tpt90)
REVERT: C   60 PHE cc_start: 0.8236 (p90) cc_final: 0.8033 (p90)
REVERT: C   99 GLU cc_start: 0.7526 (tt0) cc_final: 0.7156 (tm-30)
REVERT: D   36 SER cc_start: 0.7868 (m) cc_final: 0.7627 (p)
REVERT: D   47 LYS cc_start: 0.9099 (mttm) cc_final: 0.7734 (pptt)
REVERT: D   48 GLU cc_start: 0.6822 (pp20) cc_final: 0.6596 (tp30)
REVERT: D   53 GLN cc_start: 0.8780 (mt0) cc_final: 0.8447 (tt0)
REVERT: E  112 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6991 (ptp-110)
REVERT: E  148 GLU cc_start: 0.6794 (pm20) cc_final: 0.6040 (pm20)
REVERT: E  223 ASN cc_start: 0.7697 (p0) cc_final: 0.7078 (t0)
REVERT: E  229 GLN cc_start: 0.8581 (tt0) cc_final: 0.8214 (tp40)
REVERT: F  148 GLU cc_start: 0.6479 (pm20) cc_final: 0.5784 (pm20)
REVERT: F  223 ASN cc_start: 0.7546 (p0) cc_final: 0.6652 (t0)
REVERT: F  255 LEU cc_start: 0.9127 (tp) cc_final: 0.8702 (mm)
  outliers start: 68
  outliers final: 47
  residues processed: 351
  average time/residue: 0.3001
  time to fit residues: 138.5625
Evaluate side-chains
  332 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 283
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
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   69 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  225 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  177 MET
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  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   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  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   54 LYS
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  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  177 MET
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:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 119 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    3.5990

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

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

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.095228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.083608 restraints weight = 38251.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.085364 restraints weight = 22526.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.086740 restraints weight = 15563.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.8339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.724  11454  Z= 3.478
  Angle     :  1.092  27.984  15630  Z= 0.524
  Chirality :  0.052   0.345   1830
  Planarity :  0.007   0.127   2028
  Dihedral  :  5.577  36.317   1620
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 22.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 22.14 %
    Favored  : 71.54 %
  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:  0.22 (0.21), residues: 1500
  helix:  0.25 (0.69), residues: 54
  sheet:  0.60 (0.21), residues: 630
  loop : -0.15 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  26 
 HIS   0.028   0.003   HIS A  46 
 PHE   0.014   0.002   PHE A  60 
 TYR   0.020   0.002   TYR B 146 
 ARG   0.009   0.001   ARG D  27 

*********************** 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
  356 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 282
  time to evaluate  : 1.271 
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: 0.8849 (OUTLIER) cc_final: 0.8171 (mttt)
REVERT: A   99 GLU cc_start: 0.8592 (tt0) cc_final: 0.8342 (tm-30)
REVERT: A  148 GLU cc_start: 0.7412 (pm20) cc_final: 0.7012 (pm20)
REVERT: A  211 ASP cc_start: 0.8880 (t0) cc_final: 0.8626 (t0)
REVERT: B   85 TYR cc_start: 0.8494 (m-80) cc_final: 0.8205 (m-80)
REVERT: B   99 GLU cc_start: 0.8438 (tt0) cc_final: 0.7881 (tm-30)
REVERT: C   45 GLU cc_start: 0.8636 (pm20) cc_final: 0.8306 (pm20)
REVERT: C   46 HIS cc_start: 0.7855 (t70) cc_final: 0.7555 (t70)
REVERT: C   58 ARG cc_start: 0.8847 (tpt90) cc_final: 0.8543 (tpt90)
REVERT: C   60 PHE cc_start: 0.8478 (p90) cc_final: 0.8237 (p90)
REVERT: C   99 GLU cc_start: 0.7869 (tt0) cc_final: 0.7537 (tm-30)
REVERT: C  207 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8920 (ttpp)
REVERT: C  211 ASP cc_start: 0.8877 (t0) cc_final: 0.8568 (t0)
REVERT: C  223 ASN cc_start: 0.5498 (t0) cc_final: 0.5250 (t0)
REVERT: C  228 MET cc_start: 0.8454 (mtt) cc_final: 0.8231 (mtt)
REVERT: D   53 GLN cc_start: 0.8769 (mt0) cc_final: 0.8311 (tt0)
REVERT: D   99 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: E  148 GLU cc_start: 0.6879 (pm20) cc_final: 0.6332 (pm20)
REVERT: F   84 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8955 (mp)
REVERT: F  223 ASN cc_start: 0.7830 (p0) cc_final: 0.6716 (t0)
REVERT: F  224 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8696 (t)
REVERT: F  228 MET cc_start: 0.8687 (mtp) cc_final: 0.8474 (mtp)
REVERT: F  255 LEU cc_start: 0.9238 (tp) cc_final: 0.8807 (mm)
  outliers start: 74
  outliers final: 52
  residues processed: 321
  average time/residue: 0.2971
  time to fit residues: 127.0827
Evaluate side-chains
  293 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 238
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
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   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  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  254 GLN
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  177 MET
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain C residue   32 VAL
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   79 ASN
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   35 MET
Chi-restraints excluded: chain D residue   44 VAL
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  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   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  112 ARG
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   54 LYS
Chi-restraints excluded: chain F residue   60 PHE
Chi-restraints excluded: chain F residue   65 THR
Chi-restraints excluded: chain F residue   84 LEU
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:    4.9990
   chunk 118 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   chunk 145 optimal weight:    6.9990
   chunk 110 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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
C  79 ASN
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 115 ASN
** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  79 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.090369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.078591 restraints weight = 39932.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.080314 restraints weight = 23006.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.081418 restraints weight = 15830.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.9290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.725  11454  Z= 3.492
  Angle     :  1.198  28.131  15630  Z= 0.568
  Chirality :  0.053   0.312   1830
  Planarity :  0.007   0.118   2028
  Dihedral  :  6.224  42.203   1620
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 24.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 23.76 %
    Favored  : 69.32 %
  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: -0.21 (0.21), residues: 1500
  helix: -0.59 (0.64), residues: 54
  sheet:  0.47 (0.20), residues: 678
  loop : -0.62 (0.20), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP C  26 
 HIS   0.008   0.002   HIS F  46 
 PHE   0.015   0.002   PHE F 163 
 TYR   0.020   0.002   TYR B 146 
 ARG   0.010   0.001   ARG D 112 

*********************** 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
  333 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 252
  time to evaluate  : 1.324 
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: A   54 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8415 (mttt)
REVERT: A   58 ARG cc_start: 0.8517 (ttt-90) cc_final: 0.7949 (ttp80)
REVERT: A   99 GLU cc_start: 0.8738 (tt0) cc_final: 0.8434 (tm-30)
REVERT: A  148 GLU cc_start: 0.7343 (pm20) cc_final: 0.6845 (pm20)
REVERT: A  211 ASP cc_start: 0.8849 (t0) cc_final: 0.8568 (t0)
REVERT: B   85 TYR cc_start: 0.8615 (m-80) cc_final: 0.8405 (m-80)
REVERT: B   99 GLU cc_start: 0.8498 (tt0) cc_final: 0.8033 (tm-30)
REVERT: B  100 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8028 (p)
REVERT: C   45 GLU cc_start: 0.8676 (pm20) cc_final: 0.8306 (pm20)
REVERT: C   46 HIS cc_start: 0.7966 (t70) cc_final: 0.7708 (t70)
REVERT: C   58 ARG cc_start: 0.8788 (tpt90) cc_final: 0.8527 (tpt-90)
REVERT: C   72 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8768 (pp)
REVERT: C   99 GLU cc_start: 0.8232 (tt0) cc_final: 0.7911 (tm-30)
REVERT: C  228 MET cc_start: 0.8612 (mtt) cc_final: 0.8385 (mtt)
REVERT: D   99 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: D  211 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8850 (t0)
REVERT: E  115 ASN cc_start: 0.8711 (m-40) cc_final: 0.8381 (m-40)
REVERT: E  148 GLU cc_start: 0.6767 (pm20) cc_final: 0.6272 (pm20)
  outliers start: 81
  outliers final: 65
  residues processed: 301
  average time/residue: 0.2982
  time to fit residues: 118.7196
Evaluate side-chains
  305 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 236
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
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   65 THR
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  177 MET
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  254 GLN
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   68 VAL
Chi-restraints excluded: chain B residue   69 ASN
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  190 LYS
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain C residue   32 VAL
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   72 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   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   68 VAL
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  211 ASP
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  111 ILE
Chi-restraints excluded: chain E residue  112 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  149 VAL
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   42 GLU
Chi-restraints excluded: chain F residue   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   58 ARG
Chi-restraints excluded: chain F residue   60 PHE
Chi-restraints excluded: chain F residue   65 THR
Chi-restraints excluded: chain F residue  216 LEU
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:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 92 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 35 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 142 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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
C  38 GLN
C  53 GLN
C  79 ASN
D  53 GLN
E  53 GLN
** 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.090526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.078699 restraints weight = 39162.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.080385 restraints weight = 22297.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.081722 restraints weight = 15048.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.9469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.719  11454  Z= 3.467
  Angle     :  1.143  28.262  15630  Z= 0.537
  Chirality :  0.052   0.275   1830
  Planarity :  0.006   0.095   2028
  Dihedral  :  5.813  42.625   1620
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 22.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 25.04 %
    Favored  : 68.89 %
  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: -0.12 (0.21), residues: 1500
  helix: -0.19 (0.63), residues: 54
  sheet:  0.55 (0.20), residues: 672
  loop : -0.61 (0.21), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  26 
 HIS   0.019   0.002   HIS A  46 
 PHE   0.016   0.001   PHE E 249 
 TYR   0.018   0.002   TYR B  50 
 ARG   0.007   0.001   ARG F  27 

*********************** 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
  337 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 266
  time to evaluate  : 1.498 
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   25 LYS cc_start: 0.8803 (mmmm) cc_final: 0.8472 (tptp)
REVERT: A   54 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8039 (mttt)
REVERT: A   58 ARG cc_start: 0.8546 (ttt-90) cc_final: 0.8286 (tmm160)
REVERT: A   99 GLU cc_start: 0.8770 (tt0) cc_final: 0.8488 (tm-30)
REVERT: A  141 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7852 (ttm-80)
REVERT: A  148 GLU cc_start: 0.7329 (pm20) cc_final: 0.6913 (pm20)
REVERT: A  211 ASP cc_start: 0.8850 (t0) cc_final: 0.8507 (t0)
REVERT: B   85 TYR cc_start: 0.8624 (m-80) cc_final: 0.8395 (m-80)
REVERT: B   99 GLU cc_start: 0.8571 (tt0) cc_final: 0.8099 (tm-30)
REVERT: B  100 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8032 (p)
REVERT: C   45 GLU cc_start: 0.8620 (pm20) cc_final: 0.8262 (pm20)
REVERT: C   46 HIS cc_start: 0.7902 (t70) cc_final: 0.7624 (t70)
REVERT: C   58 ARG cc_start: 0.8743 (tpt90) cc_final: 0.8511 (tpt-90)
REVERT: C   64 LYS cc_start: 0.8273 (mttt) cc_final: 0.8049 (mttp)
REVERT: C   99 GLU cc_start: 0.8198 (tt0) cc_final: 0.7914 (tm-30)
REVERT: C  228 MET cc_start: 0.8457 (mtt) cc_final: 0.8182 (mtt)
REVERT: D   99 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: D  192 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.9026 (tp)
REVERT: E  115 ASN cc_start: 0.8694 (m-40) cc_final: 0.8312 (m-40)
REVERT: E  148 GLU cc_start: 0.6713 (pm20) cc_final: 0.6193 (pm20)
REVERT: E  173 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8717 (mtmm)
REVERT: F  188 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8657 (tpp80)
REVERT: F  204 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7288 (mm-30)
REVERT: F  255 LEU cc_start: 0.9374 (tp) cc_final: 0.8947 (mm)
  outliers start: 71
  outliers final: 54
  residues processed: 303
  average time/residue: 0.3393
  time to fit residues: 135.4754
Evaluate side-chains
  304 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 247
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
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   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  177 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  254 GLN
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   46 HIS
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   60 PHE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue  100 VAL
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   79 ASN
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain D residue   19 VAL
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  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   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  112 ARG
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   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  213 LEU
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:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0030
   chunk 5 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9980
   chunk 89 optimal weight:   50.0000
   chunk 70 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 142 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    3.3996

-------------------------------------------------------------------------------
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  79 ASN
** 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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.089466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.077728 restraints weight = 39095.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.079410 restraints weight = 22202.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.080718 restraints weight = 14990.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.9694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.721  11454  Z= 3.471
  Angle     :  1.135  29.175  15630  Z= 0.538
  Chirality :  0.052   0.345   1830
  Planarity :  0.006   0.092   2028
  Dihedral  :  5.909  38.067   1620
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 21.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 25.90 %
    Favored  : 67.44 %
  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: -0.21 (0.21), residues: 1500
  helix:  0.07 (0.65), residues: 54
  sheet:  0.47 (0.20), residues: 672
  loop : -0.67 (0.21), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  26 
 HIS   0.018   0.002   HIS A  46 
 PHE   0.014   0.002   PHE F 163 
 TYR   0.032   0.002   TYR F  85 
 ARG   0.009   0.001   ARG B  27 

*********************** 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
  329 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 251
  time to evaluate  : 1.285 
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   25 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8450 (tptp)
REVERT: A   54 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8443 (mttt)
REVERT: A   58 ARG cc_start: 0.8546 (ttt-90) cc_final: 0.8289 (tmm160)
REVERT: A   99 GLU cc_start: 0.8713 (tt0) cc_final: 0.8449 (tm-30)
REVERT: A  148 GLU cc_start: 0.7354 (pm20) cc_final: 0.6867 (pm20)
REVERT: A  211 ASP cc_start: 0.8839 (t0) cc_final: 0.8530 (t0)
REVERT: B   85 TYR cc_start: 0.8636 (m-80) cc_final: 0.8381 (m-80)
REVERT: B   99 GLU cc_start: 0.8580 (tt0) cc_final: 0.8141 (tm-30)
REVERT: B  100 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8045 (p)
REVERT: C   42 GLU cc_start: 0.8482 (pm20) cc_final: 0.8225 (pm20)
REVERT: C   45 GLU cc_start: 0.8600 (pm20) cc_final: 0.8221 (pm20)
REVERT: C   46 HIS cc_start: 0.7957 (t70) cc_final: 0.7655 (t70)
REVERT: C   64 LYS cc_start: 0.8297 (mttt) cc_final: 0.8037 (mttp)
REVERT: C  211 ASP cc_start: 0.8876 (t0) cc_final: 0.8196 (t0)
REVERT: D   99 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: E  115 ASN cc_start: 0.8698 (m-40) cc_final: 0.8367 (m-40)
REVERT: F  188 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8632 (tpp80)
REVERT: F  204 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7304 (mm-30)
REVERT: F  255 LEU cc_start: 0.9361 (tp) cc_final: 0.9118 (mm)
  outliers start: 78
  outliers final: 67
  residues processed: 292
  average time/residue: 0.3142
  time to fit residues: 120.3137
Evaluate side-chains
  314 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 245
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
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   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  177 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  254 GLN
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   60 PHE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   69 ASN
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue  100 VAL
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   67 THR
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   45 GLU
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   68 VAL
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   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  111 ILE
Chi-restraints excluded: chain E residue  112 ARG
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain E residue  149 VAL
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   65 THR
Chi-restraints excluded: chain F residue  213 LEU
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:    8.9990
   chunk 70 optimal weight:    4.9990
   chunk 142 optimal weight:    1.9990
   chunk 145 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 130 optimal weight:    8.9990
   chunk 141 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 148 optimal weight:    5.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  79 ASN
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  53 GLN
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
** F 182 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 = 0.3371 r_free = 0.3371 target = 0.091478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.079785 restraints weight = 39444.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.081491 restraints weight = 22799.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.082730 restraints weight = 15560.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.9881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.722  11454  Z= 3.474
  Angle     :  1.139  28.880  15630  Z= 0.544
  Chirality :  0.052   0.289   1830
  Planarity :  0.006   0.092   2028
  Dihedral  :  6.134  39.545   1620
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 22.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 27.09 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

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: -0.34 (0.21), residues: 1500
  helix:  0.24 (0.68), residues: 54
  sheet:  0.39 (0.20), residues: 672
  loop : -0.79 (0.21), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  26 
 HIS   0.019   0.002   HIS A  46 
 PHE   0.017   0.002   PHE C  60 
 TYR   0.027   0.002   TYR F  85 
 ARG   0.009   0.001   ARG B  27 

*********************** 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
  329 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 252
  time to evaluate  : 1.214 
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: A   43 LYS cc_start: 0.8444 (tptt) cc_final: 0.8104 (tptt)
REVERT: A   53 GLN cc_start: 0.8353 (mt0) cc_final: 0.8139 (mt0)
REVERT: A   54 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8321 (mttt)
REVERT: A   58 ARG cc_start: 0.8546 (ttt-90) cc_final: 0.8148 (ttp80)
REVERT: A   99 GLU cc_start: 0.8640 (tt0) cc_final: 0.8284 (tm-30)
REVERT: A  141 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7879 (ttm-80)
REVERT: A  148 GLU cc_start: 0.7249 (pm20) cc_final: 0.6870 (pm20)
REVERT: A  211 ASP cc_start: 0.8822 (t0) cc_final: 0.8499 (t0)
REVERT: B   60 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8045 (p90)
REVERT: B   99 GLU cc_start: 0.8528 (tt0) cc_final: 0.8151 (tm-30)
REVERT: B  100 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8109 (p)
REVERT: C   45 GLU cc_start: 0.8473 (pm20) cc_final: 0.8137 (pm20)
REVERT: C   46 HIS cc_start: 0.7848 (t70) cc_final: 0.7512 (t70)
REVERT: C   99 GLU cc_start: 0.8271 (tt0) cc_final: 0.7986 (tm-30)
REVERT: C  211 ASP cc_start: 0.8882 (t0) cc_final: 0.8209 (t0)
REVERT: D   99 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8133 (tm-30)
REVERT: E   60 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7943 (p90)
REVERT: E  115 ASN cc_start: 0.8703 (m-40) cc_final: 0.8366 (m110)
REVERT: F   49 SER cc_start: 0.8030 (t) cc_final: 0.7680 (p)
REVERT: F   91 LYS cc_start: 0.8337 (mmmt) cc_final: 0.8029 (mtmt)
REVERT: F  112 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7259 (mmt-90)
REVERT: F  255 LEU cc_start: 0.9315 (tp) cc_final: 0.9099 (mm)
  outliers start: 77
  outliers final: 67
  residues processed: 292
  average time/residue: 0.3132
  time to fit residues: 120.3886
Evaluate side-chains
  301 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 229
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
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   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  177 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  254 GLN
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   46 HIS
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   60 PHE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  100 VAL
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   67 THR
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   44 VAL
Chi-restraints excluded: chain D residue   45 GLU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   50 TYR
Chi-restraints excluded: chain D residue   54 LYS
Chi-restraints excluded: chain D residue   67 THR
Chi-restraints excluded: chain D residue   68 VAL
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  111 ILE
Chi-restraints excluded: chain E residue  112 ARG
Chi-restraints excluded: chain E residue  128 SER
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   46 HIS
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   60 PHE
Chi-restraints excluded: chain F residue  112 ARG
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:    5.9990
   chunk 14 optimal weight:   50.0000
   chunk 133 optimal weight:    0.2980
   chunk 87 optimal weight:   10.0000
   chunk 83 optimal weight:    0.3980
   chunk 13 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 134 optimal weight:    7.9990
   chunk 135 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  79 ASN
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
** F 182 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 = 0.3379 r_free = 0.3379 target = 0.091877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.080140 restraints weight = 39397.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081873 restraints weight = 22194.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.083245 restraints weight = 15061.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          1.0027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.721  11454  Z= 3.468
  Angle     :  1.121  28.976  15630  Z= 0.536
  Chirality :  0.052   0.295   1830
  Planarity :  0.006   0.089   2028
  Dihedral  :  6.078  35.201   1620
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 22.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 28.03 %
    Favored  : 66.15 %
  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: -0.36 (0.21), residues: 1500
  helix:  0.17 (0.67), residues: 54
  sheet:  0.38 (0.20), residues: 672
  loop : -0.79 (0.21), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  26 
 HIS   0.021   0.002   HIS A  46 
 PHE   0.014   0.001   PHE F 163 
 TYR   0.020   0.002   TYR B 146 
 ARG   0.009   0.001   ARG B  27 

********************** 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
  317 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 249
  time to evaluate  : 1.347 
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   43 LYS cc_start: 0.8447 (tptt) cc_final: 0.8084 (tptt)
REVERT: A   53 GLN cc_start: 0.8330 (mt0) cc_final: 0.8099 (mt0)
REVERT: A   54 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8326 (mttt)
REVERT: A   99 GLU cc_start: 0.8698 (tt0) cc_final: 0.8283 (tm-30)
REVERT: A  141 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7859 (ttm-80)
REVERT: A  148 GLU cc_start: 0.7275 (pm20) cc_final: 0.6874 (pm20)
REVERT: B   99 GLU cc_start: 0.8508 (tt0) cc_final: 0.8027 (tm-30)
REVERT: B  100 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8129 (p)
REVERT: C   45 GLU cc_start: 0.8432 (pm20) cc_final: 0.8084 (pm20)
REVERT: C   46 HIS cc_start: 0.7885 (t70) cc_final: 0.7556 (t70)
REVERT: C  211 ASP cc_start: 0.8896 (t0) cc_final: 0.8209 (t0)
REVERT: D   58 ARG cc_start: 0.8277 (tpt-90) cc_final: 0.8066 (tpt-90)
REVERT: D   99 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: E   60 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7906 (p90)
REVERT: E  115 ASN cc_start: 0.8678 (m-40) cc_final: 0.8351 (m110)
REVERT: F   91 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8035 (mtmt)
REVERT: F  112 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7278 (mmt-90)
  outliers start: 68
  outliers final: 60
  residues processed: 284
  average time/residue: 0.3259
  time to fit residues: 120.9433
Evaluate side-chains
  290 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 226
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
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   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  177 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  254 GLN
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   68 VAL
Chi-restraints excluded: chain B residue   79 ASN
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  100 VAL
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   67 THR
Chi-restraints excluded: chain C residue   79 ASN
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  177 MET
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   32 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   50 TYR
Chi-restraints excluded: chain D residue   54 LYS
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  112 ARG
Chi-restraints excluded: chain E residue  149 VAL
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   60 PHE
Chi-restraints excluded: chain F residue  112 ARG
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:    0.9990
   chunk 117 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 80 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 15 optimal weight:    0.4980
   chunk 40 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 87 optimal weight:    9.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    3.8988

-------------------------------------------------------------------------------
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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  79 ASN
** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
** F 182 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 = 0.3324 r_free = 0.3324 target = 0.089576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.077811 restraints weight = 39162.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.079517 restraints weight = 22299.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.080859 restraints weight = 15078.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          1.0201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.047   1.722  11454  Z= 3.476
  Angle     :  1.172  28.891  15630  Z= 0.561
  Chirality :  0.052   0.283   1830
  Planarity :  0.007   0.091   2028
  Dihedral  :  6.342  38.308   1620
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 23.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 28.12 %
    Favored  : 65.64 %
  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: -0.56 (0.21), residues: 1500
  helix:  0.02 (0.69), residues: 54
  sheet:  0.28 (0.20), residues: 660
  loop : -0.95 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  26 
 HIS   0.021   0.002   HIS A  46 
 PHE   0.020   0.002   PHE A  60 
 TYR   0.021   0.002   TYR A  50 
 ARG   0.009   0.001   ARG B  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3762.35 seconds
wall clock time: 69 minutes 45.01 seconds (4185.01 seconds total)