Starting phenix.real_space_refine
on Mon Jul 28 16:49:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9x_22755/07_2025/7k9x_22755.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9x_22755/07_2025/7k9x_22755.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k9x_22755/07_2025/7k9x_22755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9x_22755/07_2025/7k9x_22755.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9x_22755/07_2025/7k9x_22755.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9x_22755/07_2025/7k9x_22755.cif"
  }
  resolution = 3.8
  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=   0.003
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      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.64, per 1000 atoms: 0.54
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (97.37, 79.17, 106.47, 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      44     16.00
     O    1980      8.00
     N    1860      7.00
     C    6588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.06
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      55.7% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 24
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 92 through 100
      removed outlier: 3.729A  pdb=" N   LYS B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 219
      removed outlier: 3.539A  pdb=" N   CYS B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 275 through 287
      removed outlier: 3.637A  pdb=" N   ALA B 279 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   SER B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 3.706A  pdb=" N   GLN B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 340
    Processing helix  chain 'A' and resid 8 through 24
    Processing helix  chain 'A' and resid 35 through 47
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.730A  pdb=" N   LYS A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.539A  pdb=" N   CYS A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 258
    Processing helix  chain 'A' and resid 275 through 287
      removed outlier: 3.636A  pdb=" N   ALA A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   SER A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 3.705A  pdb=" N   GLN A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 340
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 35 through 47
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 80 through 85
    Processing helix  chain 'C' and resid 92 through 100
      removed outlier: 3.729A  pdb=" N   LYS C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 219
      removed outlier: 3.538A  pdb=" N   CYS C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 258
    Processing helix  chain 'C' and resid 275 through 287
      removed outlier: 3.637A  pdb=" N   ALA C 279 " --> pdb=" O   SER C 275 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   SER C 280 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 3.705A  pdb=" N   GLN C 306 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 340
    Processing helix  chain 'D' and resid 8 through 24
    Processing helix  chain 'D' and resid 35 through 47
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 92 through 100
      removed outlier: 3.729A  pdb=" N   LYS D 100 " --> pdb=" O   VAL D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
      removed outlier: 3.558A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 219
      removed outlier: 3.539A  pdb=" N   CYS D 201 " --> pdb=" O   ASP D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 258
    Processing helix  chain 'D' and resid 275 through 287
      removed outlier: 3.637A  pdb=" N   ALA D 279 " --> pdb=" O   SER D 275 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   SER D 280 " --> pdb=" O   GLU D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 3.706A  pdb=" N   GLN D 306 " --> pdb=" O   GLY D 302 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 340
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32
      removed outlier: 7.121A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE B 185 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   GLU B 187 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLU B 189 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   CYS B 149 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU B 191 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA B  31 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32
      removed outlier: 7.121A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE A 185 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A  31 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32
      removed outlier: 7.120A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA C  32 " --> pdb=" O   LEU C  78 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL C 104 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA C 145 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ILE C 106 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE C 185 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA C 145 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   GLU C 187 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP C 147 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLU C 189 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   CYS C 149 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   LEU C 191 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LEU C 151 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA C  31 " --> pdb=" O   TYR C 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 7.120A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   ALA D 145 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ILE D 106 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ILE D 185 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA D 145 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   GLU D 187 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP D 147 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLU D 189 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   CYS D 149 " --> pdb=" O   GLU D 189 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   LEU D 191 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LEU D 151 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA D  31 " --> pdb=" O   TYR D 301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    564 hydrogen bonds defined for protein.
    1608 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.98

  Time building geometry restraints manager: 3.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3443
        1.34 -     1.46: 1851
        1.46 -     1.57: 5322
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   ASN D  70 "
       pdb=" N   PRO D  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.92e+00
  bond pdb=" C   ASN C  70 "
       pdb=" N   PRO C  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.87e+00
  bond pdb=" C   ASN B  70 "
       pdb=" N   PRO B  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.77e+00
  bond pdb=" C   ASN A  70 "
       pdb=" N   PRO A  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.74e+00
  bond pdb=" CB  GLU B  14 "
       pdb=" CG  GLU B  14 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.42e+00
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 13401
        1.63 -     3.25: 883
        3.25 -     4.88: 115
        4.88 -     6.50: 53
        6.50 -     8.13: 12
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" C   ASN D 319 "
        pdb=" N   LEU D 320 "
        pdb=" CA  LEU D 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.32   -8.13 1.59e+00 3.96e-01 2.61e+01
  angle pdb=" C   ASN A 319 "
        pdb=" N   LEU A 320 "
        pdb=" CA  LEU A 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.31   -8.12 1.59e+00 3.96e-01 2.61e+01
  angle pdb=" C   ASN B 319 "
        pdb=" N   LEU B 320 "
        pdb=" CA  LEU B 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.27   -8.08 1.59e+00 3.96e-01 2.58e+01
  angle pdb=" C   ASN C 319 "
        pdb=" N   LEU C 320 "
        pdb=" CA  LEU C 320 "
      ideal   model   delta    sigma   weight residual
     121.19  129.26   -8.07 1.59e+00 3.96e-01 2.58e+01
  angle pdb=" CA  GLU C  49 "
        pdb=" CB  GLU C  49 "
        pdb=" CG  GLU C  49 "
      ideal   model   delta    sigma   weight residual
     114.10  121.78   -7.68 2.00e+00 2.50e-01 1.47e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 5733
       16.52 -    33.03: 591
       33.03 -    49.55: 112
       49.55 -    66.07: 56
       66.07 -    82.58: 12
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  VAL C 264 "
           pdb=" C   VAL C 264 "
           pdb=" N   THR C 265 "
           pdb=" CA  THR C 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.69  -25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  VAL A 264 "
           pdb=" C   VAL A 264 "
           pdb=" N   THR A 265 "
           pdb=" CA  THR A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.70  -25.30     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  VAL B 264 "
           pdb=" C   VAL B 264 "
           pdb=" N   THR B 265 "
           pdb=" CA  THR B 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.72  -25.28     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1094
       0.044 -    0.088: 390
       0.088 -    0.133: 116
       0.133 -    0.177: 32
       0.177 -    0.221: 12
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  ILE B  46 "
            pdb=" CA  ILE B  46 "
            pdb=" CG1 ILE B  46 "
            pdb=" CG2 ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  ILE C  46 "
            pdb=" CA  ILE C  46 "
            pdb=" CG1 ILE C  46 "
            pdb=" CG2 ILE C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  ILE A  46 "
            pdb=" CA  ILE A  46 "
            pdb=" CG1 ILE A  46 "
            pdb=" CG2 ILE A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 329 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.45e+00
        pdb=" C   LYS D 329 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LYS D 329 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG D 330 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 329 "    0.014 2.00e-02 2.50e+03   2.91e-02 8.45e+00
        pdb=" C   LYS C 329 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LYS C 329 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG C 330 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 329 "   -0.014 2.00e-02 2.50e+03   2.90e-02 8.39e+00
        pdb=" C   LYS A 329 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LYS A 329 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 330 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2592
        2.78 -     3.31: 9896
        3.31 -     3.84: 18124
        3.84 -     4.37: 21109
        4.37 -     4.90: 35941
  Nonbonded interactions: 87662
  Sorted by model distance:
  nonbonded pdb=" O   MET D 250 "
            pdb=" OG1 THR D 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET B 250 "
            pdb=" OG1 THR B 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET C 250 "
            pdb=" OG1 THR C 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   THR B  64 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.259 3.040
  ... (remaining 87657 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     26.460
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
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      :  0.008   0.054  10672  Z= 0.353
  Angle     :  0.961   8.127  14464  Z= 0.549
  Chirality :  0.053   0.221   1644
  Planarity :  0.008   0.049   1880
  Dihedral  : 15.204  82.581   3984
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  :  6.47 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.20), residues: 1364
  helix: -1.10 (0.16), residues: 672
  sheet: -2.01 (0.33), residues: 200
  loop : -0.99 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP B 295 
 HIS   0.005   0.001   HIS C 156 
 PHE   0.017   0.003   PHE A 144 
 TYR   0.017   0.003   TYR A 213 
 ARG   0.007   0.001   ARG B 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16327 (  564)
  hydrogen bonds       : angle       6.81305 ( 1608)
  covalent geometry    : bond        0.00797 (10672)
  covalent geometry    : angle       0.96122 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 323
  time to evaluate  : 1.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8524 (p)
REVERT: B   57 PHE cc_start: 0.8580 (t80) cc_final: 0.7816 (t80)
REVERT: B   60 GLN cc_start: 0.8499 (mt0) cc_final: 0.8107 (mt0)
REVERT: B   79 PHE cc_start: 0.9009 (t80) cc_final: 0.8610 (t80)
REVERT: B  100 LYS cc_start: 0.8013 (pttt) cc_final: 0.7758 (ptmt)
REVERT: B  127 LEU cc_start: 0.8329 (mt) cc_final: 0.7370 (pt)
REVERT: B  250 MET cc_start: 0.8119 (tpp) cc_final: 0.7879 (tpt)
REVERT: B  278 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8144 (mt-10)
REVERT: B  310 LEU cc_start: 0.9174 (tp) cc_final: 0.8824 (tt)
REVERT: B  311 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9133 (tptt)
REVERT: A   49 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7140 (tm-30)
REVERT: A   57 PHE cc_start: 0.8357 (t80) cc_final: 0.7534 (t80)
REVERT: A   58 TYR cc_start: 0.8431 (t80) cc_final: 0.8086 (t80)
REVERT: A   91 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7793 (ptp-110)
REVERT: A  185 ILE cc_start: 0.9085 (mt) cc_final: 0.8854 (tt)
REVERT: A  233 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7877 (p)
REVERT: A  250 MET cc_start: 0.8164 (tpp) cc_final: 0.7879 (tpt)
REVERT: A  278 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8163 (mt-10)
REVERT: A  310 LEU cc_start: 0.9127 (tp) cc_final: 0.8813 (tt)
REVERT: A  321 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7775 (tptp)
REVERT: C   61 LEU cc_start: 0.8793 (tt) cc_final: 0.8472 (tt)
REVERT: C   86 LYS cc_start: 0.7455 (mttt) cc_final: 0.7255 (ttmm)
REVERT: C   93 PHE cc_start: 0.8954 (m-10) cc_final: 0.8732 (m-80)
REVERT: C  185 ILE cc_start: 0.9070 (mt) cc_final: 0.8747 (tt)
REVERT: C  250 MET cc_start: 0.8270 (tpp) cc_final: 0.7907 (tpt)
REVERT: C  278 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: C  310 LEU cc_start: 0.9174 (tp) cc_final: 0.8899 (tt)
REVERT: C  324 GLN cc_start: 0.7521 (mt0) cc_final: 0.6663 (tm-30)
REVERT: D   38 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8549 (p)
REVERT: D   57 PHE cc_start: 0.8556 (t80) cc_final: 0.8264 (t80)
REVERT: D  100 LYS cc_start: 0.7794 (pttt) cc_final: 0.7530 (ptmt)
REVERT: D  195 ASP cc_start: 0.8420 (p0) cc_final: 0.8064 (p0)
REVERT: D  278 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8310 (mt-10)
  outliers start: 68
  outliers final: 10
  residues processed: 364
  average time/residue: 0.2909
  time to fit residues: 138.4935
Evaluate side-chains
  225 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 210
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   49 GLU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   38 SER
Chi-restraints excluded: chain C residue   49 GLU
Chi-restraints excluded: chain C residue  271 SER
Chi-restraints excluded: chain C residue  308 SER
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   38 SER
Chi-restraints excluded: chain D residue  308 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 79 optimal weight:    0.4980
   chunk 123 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 HIS
A 125 GLN
A 168 ASN
C  80 HIS
C 125 GLN
C 339 GLN
** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 178 GLN
D 237 HIS
D 282 ASN
D 339 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.115561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.089629 restraints weight = 22265.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.092741 restraints weight = 12379.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.094831 restraints weight = 8489.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.136
  Angle     :  0.624   8.604  14464  Z= 0.323
  Chirality :  0.041   0.130   1644
  Planarity :  0.005   0.041   1880
  Dihedral  :  6.723  98.206   1494
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.40 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.01 (0.22), residues: 1364
  helix:  0.97 (0.18), residues: 684
  sheet: -1.32 (0.36), residues: 184
  loop : -0.68 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 147 
 HIS   0.004   0.001   HIS D 237 
 PHE   0.030   0.002   PHE D  79 
 TYR   0.023   0.002   TYR A 203 
 ARG   0.006   0.001   ARG A  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04523 (  564)
  hydrogen bonds       : angle       4.53548 ( 1608)
  covalent geometry    : bond        0.00299 (10672)
  covalent geometry    : angle       0.62377 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 254
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8229 (ptm-80) cc_final: 0.7570 (ptm160)
REVERT: B   57 PHE cc_start: 0.8391 (t80) cc_final: 0.8086 (t80)
REVERT: B   79 PHE cc_start: 0.8950 (t80) cc_final: 0.8644 (t80)
REVERT: B  127 LEU cc_start: 0.8346 (mt) cc_final: 0.7533 (pt)
REVERT: B  178 GLN cc_start: 0.8695 (mt0) cc_final: 0.8490 (mt0)
REVERT: B  185 ILE cc_start: 0.8917 (mt) cc_final: 0.8562 (tt)
REVERT: B  250 MET cc_start: 0.8237 (tpp) cc_final: 0.7925 (tpt)
REVERT: B  339 GLN cc_start: 0.7467 (pt0) cc_final: 0.7156 (pt0)
REVERT: A  119 ASN cc_start: 0.8648 (t0) cc_final: 0.8419 (t0)
REVERT: A  127 LEU cc_start: 0.8946 (mt) cc_final: 0.8275 (pt)
REVERT: A  185 ILE cc_start: 0.9137 (mt) cc_final: 0.8912 (tt)
REVERT: A  233 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7629 (p)
REVERT: A  308 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7880 (p)
REVERT: C   42 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7440 (mtm-85)
REVERT: C   76 VAL cc_start: 0.9683 (t) cc_final: 0.9375 (p)
REVERT: C  185 ILE cc_start: 0.9102 (mt) cc_final: 0.8810 (tt)
REVERT: C  233 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7656 (p)
REVERT: C  250 MET cc_start: 0.8407 (tpp) cc_final: 0.8033 (tpt)
REVERT: C  301 TYR cc_start: 0.7806 (m-10) cc_final: 0.7604 (m-80)
REVERT: D   57 PHE cc_start: 0.8381 (t80) cc_final: 0.7847 (t80)
REVERT: D   60 GLN cc_start: 0.8389 (mt0) cc_final: 0.8182 (mt0)
REVERT: D   79 PHE cc_start: 0.8665 (t80) cc_final: 0.8424 (t80)
REVERT: D  100 LYS cc_start: 0.7531 (ptmt) cc_final: 0.7151 (ttpt)
REVERT: D  206 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8218 (mm-30)
REVERT: D  271 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7649 (m)
  outliers start: 27
  outliers final: 13
  residues processed: 264
  average time/residue: 0.2666
  time to fit residues: 94.9750
Evaluate side-chains
  226 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 209
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  271 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 122 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B 339 GLN
A 168 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN
C  80 HIS
C 339 GLN
D 237 HIS
D 339 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.117743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.092759 restraints weight = 22731.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.096145 restraints weight = 12329.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.098325 restraints weight = 8294.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10672  Z= 0.125
  Angle     :  0.592   7.955  14464  Z= 0.303
  Chirality :  0.041   0.125   1644
  Planarity :  0.004   0.030   1880
  Dihedral  :  4.593  22.237   1474
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.65 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.71 (0.23), residues: 1364
  helix:  1.68 (0.19), residues: 680
  sheet: -0.93 (0.36), residues: 184
  loop : -0.59 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 313 
 HIS   0.008   0.001   HIS C  80 
 PHE   0.020   0.001   PHE D  79 
 TYR   0.027   0.002   TYR C 222 
 ARG   0.005   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  564)
  hydrogen bonds       : angle       4.12400 ( 1608)
  covalent geometry    : bond        0.00284 (10672)
  covalent geometry    : angle       0.59198 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 253
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8184 (ptm-80) cc_final: 0.7763 (ptm160)
REVERT: B   79 PHE cc_start: 0.8971 (t80) cc_final: 0.8716 (t80)
REVERT: B  100 LYS cc_start: 0.7293 (ptmt) cc_final: 0.6981 (ttpt)
REVERT: B  127 LEU cc_start: 0.8466 (mt) cc_final: 0.7690 (pt)
REVERT: B  185 ILE cc_start: 0.8957 (mt) cc_final: 0.8631 (tt)
REVERT: B  250 MET cc_start: 0.8259 (tpp) cc_final: 0.7995 (tpt)
REVERT: B  326 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8225 (pt0)
REVERT: A  119 ASN cc_start: 0.8604 (t0) cc_final: 0.8361 (t0)
REVERT: A  185 ILE cc_start: 0.9141 (mt) cc_final: 0.8904 (tt)
REVERT: A  283 LEU cc_start: 0.8747 (tp) cc_final: 0.8422 (mt)
REVERT: A  292 LEU cc_start: 0.7418 (mm) cc_final: 0.7158 (mp)
REVERT: A  301 TYR cc_start: 0.7470 (m-10) cc_final: 0.7082 (m-80)
REVERT: A  303 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7717 (mtp180)
REVERT: C   42 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7375 (mtm-85)
REVERT: C  185 ILE cc_start: 0.9159 (mt) cc_final: 0.8845 (tt)
REVERT: C  250 MET cc_start: 0.8313 (tpp) cc_final: 0.7974 (tpt)
REVERT: D   57 PHE cc_start: 0.8333 (t80) cc_final: 0.7801 (t80)
REVERT: D   60 GLN cc_start: 0.8382 (mt0) cc_final: 0.8177 (mt0)
REVERT: D   79 PHE cc_start: 0.8782 (t80) cc_final: 0.8541 (t80)
REVERT: D  100 LYS cc_start: 0.7346 (ptmt) cc_final: 0.7047 (ttpt)
REVERT: D  206 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8161 (mm-30)
REVERT: D  306 GLN cc_start: 0.7587 (pp30) cc_final: 0.7363 (pp30)
REVERT: D  326 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8290 (pt0)
REVERT: D  330 ARG cc_start: 0.8298 (mmp-170) cc_final: 0.8048 (mmm160)
REVERT: D  339 GLN cc_start: 0.7816 (pt0) cc_final: 0.7566 (pt0)
  outliers start: 24
  outliers final: 13
  residues processed: 259
  average time/residue: 0.2542
  time to fit residues: 90.4912
Evaluate side-chains
  220 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 205
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  326 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 126 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 125 optimal weight:    0.9990
   chunk 131 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 306 GLN
B 339 GLN
A 168 ASN
A 339 GLN
C 282 ASN
D 237 HIS
D 324 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.117713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092984 restraints weight = 22497.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.096315 restraints weight = 12302.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.098489 restraints weight = 8324.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10672  Z= 0.125
  Angle     :  0.577   7.340  14464  Z= 0.297
  Chirality :  0.041   0.223   1644
  Planarity :  0.004   0.028   1880
  Dihedral  :  4.411  19.351   1472
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.19 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.92 (0.23), residues: 1364
  helix:  1.97 (0.19), residues: 676
  sheet: -0.81 (0.32), residues: 232
  loop : -0.63 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 147 
 HIS   0.008   0.001   HIS C  80 
 PHE   0.025   0.002   PHE C  79 
 TYR   0.035   0.002   TYR C 222 
 ARG   0.007   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  564)
  hydrogen bonds       : angle       3.95782 ( 1608)
  covalent geometry    : bond        0.00285 (10672)
  covalent geometry    : angle       0.57704 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 221
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8157 (ptm-80) cc_final: 0.7736 (ptm160)
REVERT: B   79 PHE cc_start: 0.8956 (t80) cc_final: 0.8636 (t80)
REVERT: B  100 LYS cc_start: 0.7235 (ptmt) cc_final: 0.6902 (ttpt)
REVERT: B  127 LEU cc_start: 0.8571 (mt) cc_final: 0.7757 (pt)
REVERT: B  185 ILE cc_start: 0.9056 (mt) cc_final: 0.8818 (tt)
REVERT: B  250 MET cc_start: 0.8263 (tpp) cc_final: 0.7968 (tpt)
REVERT: B  326 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8147 (pt0)
REVERT: A  119 ASN cc_start: 0.8561 (t0) cc_final: 0.8344 (t0)
REVERT: A  185 ILE cc_start: 0.9087 (mt) cc_final: 0.8880 (tt)
REVERT: C   57 PHE cc_start: 0.8274 (t80) cc_final: 0.7703 (t80)
REVERT: C  127 LEU cc_start: 0.8966 (mt) cc_final: 0.8181 (pt)
REVERT: C  185 ILE cc_start: 0.9112 (mt) cc_final: 0.8812 (tt)
REVERT: C  250 MET cc_start: 0.8302 (tpp) cc_final: 0.8001 (tpt)
REVERT: C  325 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: D   57 PHE cc_start: 0.8298 (t80) cc_final: 0.7806 (t80)
REVERT: D   60 GLN cc_start: 0.8357 (mt0) cc_final: 0.8150 (mt0)
REVERT: D  100 LYS cc_start: 0.7383 (ptmt) cc_final: 0.7033 (ttpt)
REVERT: D  271 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7467 (m)
REVERT: D  310 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8806 (mt)
  outliers start: 36
  outliers final: 25
  residues processed: 240
  average time/residue: 0.3049
  time to fit residues: 102.4273
Evaluate side-chains
  223 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  310 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:    0.4980
   chunk 134 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 115 optimal weight:    0.6980
   chunk 114 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN
B 339 GLN
A 168 ASN
A 282 ASN
C  80 HIS
C 282 ASN
C 339 GLN
D 339 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.118322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.093183 restraints weight = 22277.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.096522 restraints weight = 12209.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.098688 restraints weight = 8284.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10672  Z= 0.121
  Angle     :  0.574   7.017  14464  Z= 0.294
  Chirality :  0.041   0.192   1644
  Planarity :  0.004   0.031   1880
  Dihedral  :  4.309  18.325   1472
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 17.18 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.23), residues: 1364
  helix:  2.12 (0.19), residues: 684
  sheet: -0.79 (0.32), residues: 232
  loop : -0.60 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 313 
 HIS   0.005   0.001   HIS D 237 
 PHE   0.035   0.002   PHE A  79 
 TYR   0.037   0.002   TYR A 222 
 ARG   0.006   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  564)
  hydrogen bonds       : angle       3.85521 ( 1608)
  covalent geometry    : bond        0.00280 (10672)
  covalent geometry    : angle       0.57416 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 230
  time to evaluate  : 4.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7683 (ptm160)
REVERT: B   79 PHE cc_start: 0.8877 (t80) cc_final: 0.8675 (t80)
REVERT: B  100 LYS cc_start: 0.7224 (ptmt) cc_final: 0.6893 (ttpt)
REVERT: B  127 LEU cc_start: 0.8631 (mt) cc_final: 0.7855 (pt)
REVERT: B  189 GLU cc_start: 0.7216 (tm-30) cc_final: 0.7002 (tm-30)
REVERT: B  250 MET cc_start: 0.8269 (tpp) cc_final: 0.7962 (tpt)
REVERT: B  325 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7983 (pp20)
REVERT: B  326 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7953 (pt0)
REVERT: A  119 ASN cc_start: 0.8606 (t0) cc_final: 0.8362 (t0)
REVERT: A  185 ILE cc_start: 0.9106 (mt) cc_final: 0.8902 (tt)
REVERT: A  206 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8072 (mm-30)
REVERT: A  222 TYR cc_start: 0.8686 (t80) cc_final: 0.8384 (t80)
REVERT: A  283 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8693 (mt)
REVERT: A  301 TYR cc_start: 0.7281 (m-80) cc_final: 0.7035 (m-80)
REVERT: C  127 LEU cc_start: 0.9016 (mt) cc_final: 0.8164 (pt)
REVERT: C  178 GLN cc_start: 0.8957 (mt0) cc_final: 0.8734 (mt0)
REVERT: C  185 ILE cc_start: 0.9098 (mt) cc_final: 0.8818 (tt)
REVERT: C  222 TYR cc_start: 0.8547 (t80) cc_final: 0.8273 (t80)
REVERT: C  242 LYS cc_start: 0.8675 (mmpt) cc_final: 0.8071 (tttm)
REVERT: C  250 MET cc_start: 0.8221 (tpp) cc_final: 0.7943 (tpt)
REVERT: C  325 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7936 (tm-30)
REVERT: D   57 PHE cc_start: 0.8290 (t80) cc_final: 0.7854 (t80)
REVERT: D   60 GLN cc_start: 0.8294 (mt0) cc_final: 0.8091 (mt0)
REVERT: D  100 LYS cc_start: 0.7376 (ptmt) cc_final: 0.6991 (ttpt)
REVERT: D  271 SER cc_start: 0.7796 (OUTLIER) cc_final: 0.7405 (m)
REVERT: D  310 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8766 (mt)
  outliers start: 44
  outliers final: 30
  residues processed: 254
  average time/residue: 0.3971
  time to fit residues: 144.1128
Evaluate side-chains
  238 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 204
  time to evaluate  : 1.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  157 THR
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  310 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   chunk 125 optimal weight:    0.4980
   chunk 132 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN
A  54 ASN
A 168 ASN
C  54 ASN
D 287 ASN
** D 339 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 = 0.3644 r_free = 0.3644 target = 0.115183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.088793 restraints weight = 22271.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.091955 restraints weight = 12499.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.093990 restraints weight = 8621.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.129
  Angle     :  0.590   7.856  14464  Z= 0.301
  Chirality :  0.041   0.173   1644
  Planarity :  0.004   0.043   1880
  Dihedral  :  4.328  18.998   1472
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 18.08 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.23), residues: 1364
  helix:  2.03 (0.19), residues: 696
  sheet: -1.14 (0.31), residues: 228
  loop : -0.24 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 147 
 HIS   0.005   0.001   HIS C  80 
 PHE   0.028   0.002   PHE A  79 
 TYR   0.029   0.002   TYR C 222 
 ARG   0.007   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03238 (  564)
  hydrogen bonds       : angle       3.88624 ( 1608)
  covalent geometry    : bond        0.00299 (10672)
  covalent geometry    : angle       0.58979 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 227
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8247 (ptm-80) cc_final: 0.7741 (ptm160)
REVERT: B   79 PHE cc_start: 0.8922 (t80) cc_final: 0.8630 (t80)
REVERT: B  127 LEU cc_start: 0.8784 (mt) cc_final: 0.7912 (pt)
REVERT: B  189 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: B  250 MET cc_start: 0.8367 (tpp) cc_final: 0.8030 (tpt)
REVERT: B  301 TYR cc_start: 0.7919 (m-10) cc_final: 0.7715 (m-10)
REVERT: B  326 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8019 (pt0)
REVERT: A  206 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8305 (mm-30)
REVERT: A  222 TYR cc_start: 0.8713 (t80) cc_final: 0.8318 (t80)
REVERT: C  127 LEU cc_start: 0.9075 (mt) cc_final: 0.8142 (pt)
REVERT: C  185 ILE cc_start: 0.9066 (mt) cc_final: 0.8832 (tt)
REVERT: C  242 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8226 (tttm)
REVERT: C  250 MET cc_start: 0.8268 (tpp) cc_final: 0.7974 (tpt)
REVERT: C  301 TYR cc_start: 0.7432 (m-80) cc_final: 0.7217 (m-80)
REVERT: D   57 PHE cc_start: 0.8226 (t80) cc_final: 0.7713 (t80)
REVERT: D   60 GLN cc_start: 0.8319 (mt0) cc_final: 0.8069 (mt0)
REVERT: D  271 SER cc_start: 0.7712 (OUTLIER) cc_final: 0.7304 (m)
REVERT: D  288 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8273 (tttm)
REVERT: D  310 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8849 (mt)
  outliers start: 44
  outliers final: 35
  residues processed: 252
  average time/residue: 0.3071
  time to fit residues: 109.6219
Evaluate side-chains
  243 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 2.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  157 THR
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  310 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 109 optimal weight:    0.0980
   chunk 65 optimal weight:   10.0000
   chunk 130 optimal weight:    0.0040
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN
B 287 ASN
A 168 ASN
C 168 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.117185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.091184 restraints weight = 22240.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094356 restraints weight = 12358.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.096435 restraints weight = 8445.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10672  Z= 0.114
  Angle     :  0.595   8.124  14464  Z= 0.307
  Chirality :  0.041   0.158   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  4.230  18.613   1472
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.14 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.23), residues: 1364
  helix:  2.10 (0.19), residues: 684
  sheet: -1.04 (0.31), residues: 228
  loop : -0.10 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 147 
 HIS   0.005   0.000   HIS D 237 
 PHE   0.009   0.001   PHE A 144 
 TYR   0.034   0.002   TYR A 301 
 ARG   0.007   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03022 (  564)
  hydrogen bonds       : angle       3.81504 ( 1608)
  covalent geometry    : bond        0.00257 (10672)
  covalent geometry    : angle       0.59513 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 232
  time to evaluate  : 1.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8112 (ptm-80) cc_final: 0.7562 (ptm160)
REVERT: B   79 PHE cc_start: 0.8827 (t80) cc_final: 0.8547 (t80)
REVERT: B  127 LEU cc_start: 0.8757 (mt) cc_final: 0.7939 (pt)
REVERT: B  189 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: B  282 ASN cc_start: 0.8700 (m-40) cc_final: 0.8489 (m-40)
REVERT: B  303 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7754 (mtp85)
REVERT: B  325 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7994 (pp20)
REVERT: B  326 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7915 (pt0)
REVERT: A   76 VAL cc_start: 0.9612 (t) cc_final: 0.9289 (p)
REVERT: A  119 ASN cc_start: 0.8679 (t0) cc_final: 0.8441 (t0)
REVERT: A  206 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8309 (mm-30)
REVERT: A  222 TYR cc_start: 0.8701 (t80) cc_final: 0.8388 (t80)
REVERT: C   34 GLU cc_start: 0.8175 (mp0) cc_final: 0.7816 (mp0)
REVERT: C  127 LEU cc_start: 0.9013 (mt) cc_final: 0.8092 (pt)
REVERT: C  185 ILE cc_start: 0.8991 (mt) cc_final: 0.8760 (tt)
REVERT: C  242 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8258 (tttm)
REVERT: C  250 MET cc_start: 0.8222 (tpp) cc_final: 0.7928 (tpt)
REVERT: C  269 PHE cc_start: 0.8466 (m-80) cc_final: 0.8263 (m-80)
REVERT: C  325 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7934 (mt-10)
REVERT: D   57 PHE cc_start: 0.8224 (t80) cc_final: 0.7567 (t80)
REVERT: D   60 GLN cc_start: 0.8289 (mt0) cc_final: 0.8015 (mt0)
REVERT: D  100 LYS cc_start: 0.7209 (ptmt) cc_final: 0.6482 (ttpt)
REVERT: D  271 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7307 (m)
REVERT: D  288 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8239 (tttm)
REVERT: D  310 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8833 (mt)
  outliers start: 38
  outliers final: 31
  residues processed: 254
  average time/residue: 0.2529
  time to fit residues: 88.8065
Evaluate side-chains
  231 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 197
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  310 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 10 optimal weight:    0.0980
   chunk 109 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0030
   chunk 80 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 121 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.118367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.092448 restraints weight = 21829.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.095634 restraints weight = 12219.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.097579 restraints weight = 8368.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.114
  Angle     :  0.603   7.710  14464  Z= 0.310
  Chirality :  0.041   0.161   1644
  Planarity :  0.004   0.027   1880
  Dihedral  :  4.190  21.300   1472
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.49 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.23), residues: 1364
  helix:  1.97 (0.19), residues: 688
  sheet: -0.90 (0.32), residues: 216
  loop :  0.03 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 295 
 HIS   0.005   0.000   HIS D 237 
 PHE   0.021   0.002   PHE D  79 
 TYR   0.043   0.002   TYR A 301 
 ARG   0.007   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03009 (  564)
  hydrogen bonds       : angle       3.84122 ( 1608)
  covalent geometry    : bond        0.00260 (10672)
  covalent geometry    : angle       0.60271 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 211
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8098 (ptm-80) cc_final: 0.7595 (ptm160)
REVERT: B   79 PHE cc_start: 0.8784 (t80) cc_final: 0.8520 (t80)
REVERT: B  127 LEU cc_start: 0.8754 (mt) cc_final: 0.7937 (pt)
REVERT: B  292 LEU cc_start: 0.7567 (mm) cc_final: 0.7306 (mp)
REVERT: B  301 TYR cc_start: 0.7890 (m-10) cc_final: 0.7492 (m-10)
REVERT: B  303 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7751 (mtp85)
REVERT: B  326 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8028 (pt0)
REVERT: B  330 ARG cc_start: 0.8275 (mmp-170) cc_final: 0.7678 (ttp-170)
REVERT: A  119 ASN cc_start: 0.8674 (t0) cc_final: 0.8443 (t0)
REVERT: A  127 LEU cc_start: 0.8957 (mt) cc_final: 0.8175 (pt)
REVERT: A  206 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8288 (mm-30)
REVERT: A  222 TYR cc_start: 0.8690 (t80) cc_final: 0.8311 (t80)
REVERT: A  269 PHE cc_start: 0.8598 (m-80) cc_final: 0.8371 (m-80)
REVERT: A  288 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8145 (ptmm)
REVERT: A  301 TYR cc_start: 0.7520 (m-80) cc_final: 0.7198 (m-80)
REVERT: C  185 ILE cc_start: 0.8942 (mt) cc_final: 0.8706 (tt)
REVERT: C  222 TYR cc_start: 0.8552 (t80) cc_final: 0.7983 (t80)
REVERT: C  242 LYS cc_start: 0.8733 (mmpt) cc_final: 0.8248 (tttm)
REVERT: C  269 PHE cc_start: 0.8472 (m-80) cc_final: 0.8226 (m-80)
REVERT: C  303 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7657 (mtp180)
REVERT: C  321 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8065 (tptp)
REVERT: D   57 PHE cc_start: 0.8169 (t80) cc_final: 0.7561 (t80)
REVERT: D   60 GLN cc_start: 0.8271 (mt0) cc_final: 0.8033 (mt0)
REVERT: D  100 LYS cc_start: 0.7180 (ptmt) cc_final: 0.6492 (ttpt)
REVERT: D  271 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7267 (m)
REVERT: D  310 LEU cc_start: 0.9037 (mt) cc_final: 0.8823 (mt)
  outliers start: 36
  outliers final: 29
  residues processed: 232
  average time/residue: 0.2375
  time to fit residues: 75.4887
Evaluate side-chains
  225 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  271 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 41 optimal weight:    8.9990
   chunk 132 optimal weight:    6.9990
   chunk 123 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 282 ASN
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 219 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.117961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.091698 restraints weight = 22210.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.094898 restraints weight = 12317.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.096940 restraints weight = 8422.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10672  Z= 0.123
  Angle     :  0.618   6.690  14464  Z= 0.319
  Chirality :  0.041   0.163   1644
  Planarity :  0.004   0.028   1880
  Dihedral  :  4.198  21.583   1472
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.31 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.23), residues: 1364
  helix:  1.99 (0.19), residues: 688
  sheet: -0.96 (0.31), residues: 228
  loop : -0.13 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 295 
 HIS   0.005   0.001   HIS D 237 
 PHE   0.013   0.001   PHE C  93 
 TYR   0.041   0.002   TYR C 301 
 ARG   0.006   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03045 (  564)
  hydrogen bonds       : angle       3.87607 ( 1608)
  covalent geometry    : bond        0.00285 (10672)
  covalent geometry    : angle       0.61784 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 210
  time to evaluate  : 2.588 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.7586 (ptm160)
REVERT: B   79 PHE cc_start: 0.8780 (t80) cc_final: 0.8524 (t80)
REVERT: B  127 LEU cc_start: 0.8789 (mt) cc_final: 0.7947 (pt)
REVERT: B  301 TYR cc_start: 0.7948 (m-10) cc_final: 0.7530 (m-10)
REVERT: B  326 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8037 (pt0)
REVERT: A  119 ASN cc_start: 0.8669 (t0) cc_final: 0.8370 (t0)
REVERT: A  127 LEU cc_start: 0.8934 (mt) cc_final: 0.8122 (pt)
REVERT: A  222 TYR cc_start: 0.8703 (t80) cc_final: 0.8244 (t80)
REVERT: A  269 PHE cc_start: 0.8563 (m-80) cc_final: 0.8294 (m-80)
REVERT: A  288 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8134 (ptmm)
REVERT: A  301 TYR cc_start: 0.7686 (m-80) cc_final: 0.7443 (m-80)
REVERT: C  185 ILE cc_start: 0.8914 (mt) cc_final: 0.8689 (tt)
REVERT: C  206 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7878 (mm-30)
REVERT: C  242 LYS cc_start: 0.8736 (mmpt) cc_final: 0.8219 (tttp)
REVERT: C  269 PHE cc_start: 0.8467 (m-80) cc_final: 0.8132 (m-80)
REVERT: C  310 LEU cc_start: 0.9069 (tp) cc_final: 0.8842 (tt)
REVERT: D   57 PHE cc_start: 0.8173 (t80) cc_final: 0.7572 (t80)
REVERT: D   60 GLN cc_start: 0.8288 (mt0) cc_final: 0.8027 (mt0)
REVERT: D  271 SER cc_start: 0.7585 (OUTLIER) cc_final: 0.7198 (m)
REVERT: D  310 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8813 (mt)
  outliers start: 37
  outliers final: 29
  residues processed: 232
  average time/residue: 0.3180
  time to fit residues: 104.0323
Evaluate side-chains
  227 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 194
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  310 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 106 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0770
   chunk 112 optimal weight:    3.9990
   overall best weight:    1.3742

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

Flipped N/Q/H residues before XYZ refinement:
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  60 GLN
C 136 GLN
** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.116211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.089907 restraints weight = 22212.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.093136 restraints weight = 12101.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.095231 restraints weight = 8215.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10672  Z= 0.144
  Angle     :  0.645   8.052  14464  Z= 0.331
  Chirality :  0.042   0.171   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  4.270  21.950   1472
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.85 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.23), residues: 1364
  helix:  1.93 (0.19), residues: 692
  sheet: -0.94 (0.32), residues: 228
  loop : -0.04 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 147 
 HIS   0.005   0.001   HIS D 237 
 PHE   0.030   0.002   PHE A  79 
 TYR   0.038   0.003   TYR A 301 
 ARG   0.009   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  564)
  hydrogen bonds       : angle       3.99045 ( 1608)
  covalent geometry    : bond        0.00339 (10672)
  covalent geometry    : angle       0.64534 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 209
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8066 (ptm-80) cc_final: 0.7632 (ptm160)
REVERT: B   79 PHE cc_start: 0.8853 (t80) cc_final: 0.8591 (t80)
REVERT: B  127 LEU cc_start: 0.8856 (mt) cc_final: 0.7964 (pt)
REVERT: B  301 TYR cc_start: 0.8043 (m-10) cc_final: 0.7614 (m-10)
REVERT: B  303 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7727 (mtp85)
REVERT: B  326 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8069 (pt0)
REVERT: B  330 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7709 (ttp-170)
REVERT: A  119 ASN cc_start: 0.8682 (t0) cc_final: 0.8372 (t0)
REVERT: A  222 TYR cc_start: 0.8766 (t80) cc_final: 0.8219 (t80)
REVERT: A  288 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8240 (ptmm)
REVERT: C  127 LEU cc_start: 0.9026 (mt) cc_final: 0.8026 (pt)
REVERT: C  206 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8034 (mm-30)
REVERT: C  222 TYR cc_start: 0.8645 (t80) cc_final: 0.8086 (t80)
REVERT: C  242 LYS cc_start: 0.8729 (mmpt) cc_final: 0.8161 (tttp)
REVERT: C  269 PHE cc_start: 0.8475 (m-80) cc_final: 0.8187 (m-80)
REVERT: C  301 TYR cc_start: 0.7431 (m-80) cc_final: 0.7066 (m-80)
REVERT: D   56 ARG cc_start: 0.7807 (ptm-80) cc_final: 0.7378 (ptm160)
REVERT: D   57 PHE cc_start: 0.8190 (t80) cc_final: 0.7838 (t80)
REVERT: D   58 TYR cc_start: 0.8438 (t80) cc_final: 0.7968 (t80)
REVERT: D  100 LYS cc_start: 0.7397 (ptmt) cc_final: 0.7082 (mtmt)
REVERT: D  271 SER cc_start: 0.7551 (OUTLIER) cc_final: 0.7154 (m)
REVERT: D  310 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8766 (mt)
  outliers start: 41
  outliers final: 36
  residues processed: 233
  average time/residue: 0.2819
  time to fit residues: 90.6246
Evaluate side-chains
  232 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 192
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  157 THR
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  310 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   chunk 135 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
C  60 GLN
** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.117093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.091394 restraints weight = 21840.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.094519 restraints weight = 12158.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.096572 restraints weight = 8344.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.4843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10672  Z= 0.127
  Angle     :  0.641   7.195  14464  Z= 0.330
  Chirality :  0.041   0.164   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  4.261  22.559   1472
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.66 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.23), residues: 1364
  helix:  1.89 (0.19), residues: 692
  sheet: -0.92 (0.32), residues: 228
  loop : -0.03 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 295 
 HIS   0.005   0.001   HIS B 237 
 PHE   0.015   0.001   PHE C  93 
 TYR   0.036   0.003   TYR A 301 
 ARG   0.009   0.000   ARG B 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  564)
  hydrogen bonds       : angle       3.94578 ( 1608)
  covalent geometry    : bond        0.00297 (10672)
  covalent geometry    : angle       0.64062 (14464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3854.50 seconds
wall clock time: 73 minutes 12.48 seconds (4392.48 seconds total)