Starting phenix.real_space_refine
on Wed Mar  4 03:32:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9x_22755/03_2026/7k9x_22755.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9x_22755/03_2026/7k9x_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_22755/03_2026/7k9x_22755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9x_22755/03_2026/7k9x_22755.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9x_22755/03_2026/7k9x_22755.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9x_22755/03_2026/7k9x_22755.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      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:
    A, C, D
  Time building chain proxies: 1.75, per 1000 atoms: 0.17
  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: 0.68
  Conformation dependent library (CDL) restraints added in 345.0 milliseconds
  

  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: 0.28
  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: 1.38

  Time building geometry restraints manager: 0.93 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  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:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.120
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.960
-------------------------------------------------------------------------------
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 : 6.27
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.001   ARG B 172 
 TYR   0.017   0.003   TYR A 213 
 PHE   0.017   0.003   PHE A 144 
 TRP   0.022   0.004   TRP B 295 
 HIS   0.005   0.001   HIS C 156 

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

*********************** 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  : 0.422 
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: 0.1247
  time to fit residues: 59.9253
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  : 0.384 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.0980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
B 237 HIS
A 125 GLN
A 168 ASN
A 220 HIS
C  60 GLN
C  80 HIS
C 125 GLN
C 220 HIS
C 306 GLN
C 339 GLN
D 168 ASN
D 178 GLN
D 237 HIS
D 282 ASN
D 324 GLN
D 339 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.116781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.091022 restraints weight = 21900.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.094267 restraints weight = 11967.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.096350 restraints weight = 8078.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.097749 restraints weight = 6281.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.098643 restraints weight = 5340.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2553

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= 0.127
  Angle     :  0.615   8.828  14464  Z= 0.317
  Chirality :  0.041   0.134   1644
  Planarity :  0.005   0.041   1880
  Dihedral  :  6.633 101.358   1494
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.76 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.22), residues: 1364
  helix:  0.86 (0.18), residues: 708
  sheet: -1.28 (0.36), residues: 184
  loop : -0.64 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  56 
 TYR   0.025   0.002   TYR A 203 
 PHE   0.029   0.002   PHE D  79 
 TRP   0.005   0.001   TRP A 147 
 HIS   0.005   0.001   HIS D 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10672)
  covalent geometry    : angle       0.61477 (14464)
  hydrogen bonds       : bond        0.04124 (  564)
  hydrogen bonds       : angle       4.42904 ( 1608)

*********************** 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
  293 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 266
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8189 (ptm-80) cc_final: 0.7173 (ptm-80)
REVERT: B   57 PHE cc_start: 0.8413 (t80) cc_final: 0.8040 (t80)
REVERT: B   60 GLN cc_start: 0.8402 (mt0) cc_final: 0.8124 (mt0)
REVERT: B   79 PHE cc_start: 0.8944 (t80) cc_final: 0.8648 (t80)
REVERT: B  127 LEU cc_start: 0.8349 (mt) cc_final: 0.7566 (pt)
REVERT: B  178 GLN cc_start: 0.8652 (mt0) cc_final: 0.8441 (mt0)
REVERT: B  185 ILE cc_start: 0.8876 (mt) cc_final: 0.8518 (tt)
REVERT: B  250 MET cc_start: 0.8192 (tpp) cc_final: 0.7972 (tpt)
REVERT: B  339 GLN cc_start: 0.7355 (pt0) cc_final: 0.7040 (pt0)
REVERT: A  119 ASN cc_start: 0.8589 (t0) cc_final: 0.8374 (t0)
REVERT: A  127 LEU cc_start: 0.8912 (mt) cc_final: 0.8290 (pt)
REVERT: A  185 ILE cc_start: 0.9119 (mt) cc_final: 0.8899 (tt)
REVERT: A  233 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7606 (p)
REVERT: A  250 MET cc_start: 0.8228 (tpp) cc_final: 0.7925 (tpt)
REVERT: A  308 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7988 (p)
REVERT: C   42 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7399 (mtm-85)
REVERT: C  185 ILE cc_start: 0.9070 (mt) cc_final: 0.8808 (tt)
REVERT: C  222 TYR cc_start: 0.8787 (t80) cc_final: 0.8351 (t80)
REVERT: C  233 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7611 (p)
REVERT: C  250 MET cc_start: 0.8400 (tpp) cc_final: 0.8080 (tpt)
REVERT: D   57 PHE cc_start: 0.8369 (t80) cc_final: 0.7841 (t80)
REVERT: D   79 PHE cc_start: 0.8630 (t80) cc_final: 0.8374 (t80)
REVERT: D  100 LYS cc_start: 0.7444 (ptmt) cc_final: 0.7114 (ttpt)
REVERT: D  206 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8200 (mm-30)
REVERT: D  339 GLN cc_start: 0.7810 (pt0) cc_final: 0.7513 (pt0)
  outliers start: 27
  outliers final: 14
  residues processed: 275
  average time/residue: 0.1180
  time to fit residues: 43.8380
Evaluate side-chains
  235 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 218
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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   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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    0.6980
   chunk 2 optimal weight:    7.9990
   chunk 118 optimal weight:    0.9990
   chunk 133 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 112 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 339 GLN
C  60 GLN
C  80 HIS
C 282 ASN
C 339 GLN
D  60 GLN
D 237 HIS
D 282 ASN
D 324 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.115906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.091025 restraints weight = 22751.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094331 restraints weight = 12378.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.096459 restraints weight = 8355.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.097800 restraints weight = 6505.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.098606 restraints weight = 5543.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10672  Z= 0.162
  Angle     :  0.616   8.937  14464  Z= 0.316
  Chirality :  0.042   0.130   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  4.655  21.077   1474
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.47 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.23), residues: 1364
  helix:  1.76 (0.19), residues: 680
  sheet: -1.23 (0.34), residues: 200
  loop : -0.50 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 303 
 TYR   0.027   0.002   TYR A 222 
 PHE   0.020   0.002   PHE D  79 
 TRP   0.008   0.001   TRP A 313 
 HIS   0.011   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10672)
  covalent geometry    : angle       0.61576 (14464)
  hydrogen bonds       : bond        0.03838 (  564)
  hydrogen bonds       : angle       4.19603 ( 1608)

*********************** 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
  274 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 244
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8128 (ptm-80) cc_final: 0.7131 (ptm-80)
REVERT: B   57 PHE cc_start: 0.8339 (t80) cc_final: 0.7958 (t80)
REVERT: B   60 GLN cc_start: 0.8393 (mt0) cc_final: 0.8165 (mt0)
REVERT: B  100 LYS cc_start: 0.7276 (ptmt) cc_final: 0.6957 (ttpt)
REVERT: B  250 MET cc_start: 0.8253 (tpp) cc_final: 0.7944 (tpt)
REVERT: B  271 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7766 (m)
REVERT: B  326 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8163 (pt0)
REVERT: A   42 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7283 (mmm-85)
REVERT: A  185 ILE cc_start: 0.9106 (mt) cc_final: 0.8895 (tt)
REVERT: A  206 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8106 (mm-30)
REVERT: A  222 TYR cc_start: 0.8936 (t80) cc_final: 0.8670 (t80)
REVERT: A  250 MET cc_start: 0.8217 (tpp) cc_final: 0.7931 (tpt)
REVERT: A  283 LEU cc_start: 0.8792 (tp) cc_final: 0.8398 (mt)
REVERT: A  301 TYR cc_start: 0.7638 (m-10) cc_final: 0.7195 (m-80)
REVERT: C   42 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7435 (mmm-85)
REVERT: C   49 GLU cc_start: 0.7740 (tp30) cc_final: 0.7469 (tm-30)
REVERT: C  185 ILE cc_start: 0.9129 (mt) cc_final: 0.8820 (tt)
REVERT: C  250 MET cc_start: 0.8306 (tpp) cc_final: 0.7983 (tpt)
REVERT: C  283 LEU cc_start: 0.8839 (tp) cc_final: 0.8639 (tp)
REVERT: C  301 TYR cc_start: 0.7814 (m-80) cc_final: 0.7416 (m-80)
REVERT: D  100 LYS cc_start: 0.7342 (ptmt) cc_final: 0.7019 (ttpt)
REVERT: D  271 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7595 (m)
REVERT: D  326 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8264 (pt0)
REVERT: D  330 ARG cc_start: 0.8322 (mmp-170) cc_final: 0.8025 (mmm160)
REVERT: D  339 GLN cc_start: 0.7826 (pt0) cc_final: 0.7552 (pt0)
  outliers start: 30
  outliers final: 17
  residues processed: 259
  average time/residue: 0.1001
  time to fit residues: 36.3617
Evaluate side-chains
  231 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 210
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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  271 SER
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  212 VAL
Chi-restraints excluded: chain C residue  252 THR
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  326 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 127 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN
B 306 GLN
B 339 GLN
A 168 ASN
A 282 ASN
A 306 GLN
A 339 GLN
C  80 HIS
C 282 ASN
** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 168 ASN
D 237 HIS
D 282 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.117993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.092706 restraints weight = 22556.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.096077 restraints weight = 12341.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.098266 restraints weight = 8333.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.099616 restraints weight = 6481.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.100518 restraints weight = 5534.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3537

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= 0.116
  Angle     :  0.576   7.498  14464  Z= 0.296
  Chirality :  0.041   0.131   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  4.409  20.301   1472
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.10 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.23), residues: 1364
  helix:  2.01 (0.19), residues: 684
  sheet: -0.83 (0.31), residues: 232
  loop : -0.57 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 303 
 TYR   0.024   0.002   TYR D 203 
 PHE   0.023   0.002   PHE D  79 
 TRP   0.004   0.001   TRP D 147 
 HIS   0.009   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10672)
  covalent geometry    : angle       0.57605 (14464)
  hydrogen bonds       : bond        0.03336 (  564)
  hydrogen bonds       : angle       3.93815 ( 1608)

*********************** 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
  278 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 242
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.7067 (ptm-80)
REVERT: B   57 PHE cc_start: 0.8342 (t80) cc_final: 0.7977 (t80)
REVERT: B  100 LYS cc_start: 0.7190 (ptmt) cc_final: 0.6866 (ttpt)
REVERT: B  127 LEU cc_start: 0.8602 (mt) cc_final: 0.7833 (pt)
REVERT: B  185 ILE cc_start: 0.9005 (mt) cc_final: 0.8752 (tt)
REVERT: B  250 MET cc_start: 0.8257 (tpp) cc_final: 0.7935 (tpt)
REVERT: B  271 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7691 (m)
REVERT: B  325 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: A   42 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7239 (mmm-85)
REVERT: A  119 ASN cc_start: 0.8575 (t0) cc_final: 0.8333 (t0)
REVERT: A  185 ILE cc_start: 0.9056 (mt) cc_final: 0.8849 (tt)
REVERT: A  206 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8073 (mm-30)
REVERT: A  222 TYR cc_start: 0.8905 (t80) cc_final: 0.8485 (t80)
REVERT: A  250 MET cc_start: 0.8211 (tpp) cc_final: 0.7954 (tpt)
REVERT: C  127 LEU cc_start: 0.8966 (mt) cc_final: 0.8181 (pt)
REVERT: C  185 ILE cc_start: 0.9068 (mt) cc_final: 0.8766 (tt)
REVERT: C  222 TYR cc_start: 0.8873 (t80) cc_final: 0.8372 (t80)
REVERT: C  250 MET cc_start: 0.8304 (tpp) cc_final: 0.7994 (tpt)
REVERT: C  283 LEU cc_start: 0.8874 (tp) cc_final: 0.8620 (tp)
REVERT: C  301 TYR cc_start: 0.7605 (m-10) cc_final: 0.7294 (m-10)
REVERT: C  325 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: D  100 LYS cc_start: 0.7347 (ptmt) cc_final: 0.6991 (ttpt)
REVERT: D  185 ILE cc_start: 0.9077 (mt) cc_final: 0.8876 (tt)
REVERT: D  271 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7490 (m)
REVERT: D  310 LEU cc_start: 0.9083 (mt) cc_final: 0.8804 (mt)
REVERT: D  325 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7867 (tm-30)
  outliers start: 36
  outliers final: 24
  residues processed: 266
  average time/residue: 0.0971
  time to fit residues: 36.5567
Evaluate side-chains
  234 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 208
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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  168 ASN
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain A residue   23 VAL
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  343 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain D residue   61 LEU
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 91 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 128 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 127 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B 287 ASN
B 306 GLN
B 339 GLN
A  54 ASN
A 168 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 324 GLN
A 339 GLN
C  54 ASN
C 339 GLN
D 237 HIS
D 339 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.113992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.087956 restraints weight = 22182.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.091165 restraints weight = 12092.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.093204 restraints weight = 8202.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.094367 restraints weight = 6406.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.095286 restraints weight = 5534.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10672  Z= 0.146
  Angle     :  0.596   8.042  14464  Z= 0.306
  Chirality :  0.042   0.215   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  4.404  19.120   1472
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.36 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.23), residues: 1364
  helix:  2.08 (0.19), residues: 684
  sheet: -0.77 (0.34), residues: 184
  loop : -0.52 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 303 
 TYR   0.022   0.002   TYR B 203 
 PHE   0.036   0.002   PHE A  79 
 TRP   0.005   0.001   TRP C 147 
 HIS   0.005   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10672)
  covalent geometry    : angle       0.59624 (14464)
  hydrogen bonds       : bond        0.03447 (  564)
  hydrogen bonds       : angle       3.93694 ( 1608)

*********************** 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
  268 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 218
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8211 (ptm-80) cc_final: 0.7345 (ptm-80)
REVERT: B  100 LYS cc_start: 0.7325 (ptmt) cc_final: 0.6982 (ttpt)
REVERT: B  127 LEU cc_start: 0.8807 (mt) cc_final: 0.7913 (pt)
REVERT: B  185 ILE cc_start: 0.9061 (mt) cc_final: 0.8854 (tt)
REVERT: B  189 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7043 (tm-30)
REVERT: B  250 MET cc_start: 0.8372 (tpp) cc_final: 0.8024 (tpt)
REVERT: B  271 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7654 (m)
REVERT: A   42 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7360 (mmm-85)
REVERT: A  185 ILE cc_start: 0.9042 (mt) cc_final: 0.8838 (tt)
REVERT: A  250 MET cc_start: 0.8215 (tpp) cc_final: 0.7937 (tpt)
REVERT: C  127 LEU cc_start: 0.9052 (mt) cc_final: 0.8141 (pt)
REVERT: C  185 ILE cc_start: 0.9031 (mt) cc_final: 0.8742 (tt)
REVERT: C  250 MET cc_start: 0.8334 (tpp) cc_final: 0.7972 (tpt)
REVERT: C  283 LEU cc_start: 0.8869 (tp) cc_final: 0.8654 (tp)
REVERT: C  301 TYR cc_start: 0.7818 (m-10) cc_final: 0.7524 (m-80)
REVERT: D   56 ARG cc_start: 0.7993 (ptm-80) cc_final: 0.7533 (ptm160)
REVERT: D  271 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7446 (m)
REVERT: D  310 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8815 (mt)
  outliers start: 50
  outliers final: 35
  residues processed: 249
  average time/residue: 0.0962
  time to fit residues: 34.3962
Evaluate side-chains
  245 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 207
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
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  247 GLU
Chi-restraints excluded: chain B residue  271 SER
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   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  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  151 LEU
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  297 LEU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   69 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  157 THR
Chi-restraints excluded: chain D residue  267 VAL
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 110 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 83 optimal weight:    0.7980
   chunk 23 optimal weight:    0.4980
   chunk 85 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN
A 168 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 ASN
D 168 ASN
D 237 HIS
D 287 ASN
D 339 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.115685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.088954 restraints weight = 22389.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.092159 restraints weight = 12335.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.094231 restraints weight = 8465.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.095489 restraints weight = 6664.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.096377 restraints weight = 5763.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10672  Z= 0.121
  Angle     :  0.597   8.124  14464  Z= 0.303
  Chirality :  0.041   0.180   1644
  Planarity :  0.004   0.031   1880
  Dihedral  :  4.327  20.101   1472
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.27 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.23), residues: 1364
  helix:  2.13 (0.19), residues: 684
  sheet: -0.98 (0.28), residues: 260
  loop : -0.34 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 303 
 TYR   0.040   0.002   TYR A 301 
 PHE   0.037   0.002   PHE A  79 
 TRP   0.007   0.001   TRP A 147 
 HIS   0.005   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10672)
  covalent geometry    : angle       0.59681 (14464)
  hydrogen bonds       : bond        0.03233 (  564)
  hydrogen bonds       : angle       3.84956 ( 1608)

*********************** 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
  280 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 230
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8165 (ptm-80) cc_final: 0.7303 (ptm-80)
REVERT: B  127 LEU cc_start: 0.8819 (mt) cc_final: 0.7944 (pt)
REVERT: B  189 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7224 (tm-30)
REVERT: B  271 SER cc_start: 0.7808 (OUTLIER) cc_final: 0.7506 (m)
REVERT: B  303 ARG cc_start: 0.8021 (mtp-110) cc_final: 0.7536 (mmm-85)
REVERT: B  325 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7951 (pp20)
REVERT: B  326 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8383 (pp20)
REVERT: A  119 ASN cc_start: 0.8682 (t0) cc_final: 0.8380 (t0)
REVERT: A  250 MET cc_start: 0.8191 (tpp) cc_final: 0.7920 (tpt)
REVERT: A  283 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8766 (mt)
REVERT: A  301 TYR cc_start: 0.7451 (m-80) cc_final: 0.7084 (m-80)
REVERT: C   30 LEU cc_start: 0.8687 (tt) cc_final: 0.8471 (tp)
REVERT: C  127 LEU cc_start: 0.9013 (mt) cc_final: 0.8106 (pt)
REVERT: C  222 TYR cc_start: 0.8881 (t80) cc_final: 0.8533 (t80)
REVERT: C  250 MET cc_start: 0.8265 (tpp) cc_final: 0.7941 (tpt)
REVERT: C  283 LEU cc_start: 0.8870 (tp) cc_final: 0.8644 (tp)
REVERT: C  301 TYR cc_start: 0.7574 (m-10) cc_final: 0.7309 (m-80)
REVERT: C  325 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7912 (mt-10)
REVERT: C  326 GLU cc_start: 0.7988 (pt0) cc_final: 0.7765 (mp0)
REVERT: D  271 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7326 (m)
REVERT: D  310 LEU cc_start: 0.9000 (mt) cc_final: 0.8741 (mt)
  outliers start: 50
  outliers final: 35
  residues processed: 262
  average time/residue: 0.0916
  time to fit residues: 34.1728
Evaluate side-chains
  242 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 203
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
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  168 ASN
Chi-restraints excluded: chain B residue  271 SER
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   67 ASP
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  343 THR
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  124 THR
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  212 VAL
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  297 LEU
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  157 THR
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  275 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 116 optimal weight:    4.9990
   chunk 129 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   overall best weight:    3.1788

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.110451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.084771 restraints weight = 22699.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.087672 restraints weight = 12853.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.089528 restraints weight = 8954.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.090596 restraints weight = 7137.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.091412 restraints weight = 6238.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  10672  Z= 0.245
  Angle     :  0.709   9.965  14464  Z= 0.363
  Chirality :  0.045   0.205   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  4.782  20.460   1472
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 18.71 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.23), residues: 1364
  helix:  1.98 (0.19), residues: 680
  sheet: -1.00 (0.32), residues: 208
  loop : -0.40 (0.31), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 303 
 TYR   0.044   0.003   TYR A 222 
 PHE   0.018   0.002   PHE B  79 
 TRP   0.007   0.002   TRP C 147 
 HIS   0.005   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (10672)
  covalent geometry    : angle       0.70926 (14464)
  hydrogen bonds       : bond        0.04098 (  564)
  hydrogen bonds       : angle       4.29824 ( 1608)

*********************** 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
  261 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 207
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8084 (ptm-80) cc_final: 0.7517 (ptm160)
REVERT: B  271 SER cc_start: 0.7796 (OUTLIER) cc_final: 0.7403 (m)
REVERT: B  292 LEU cc_start: 0.7545 (mm) cc_final: 0.7295 (mp)
REVERT: A  250 MET cc_start: 0.8255 (tpp) cc_final: 0.7972 (tpt)
REVERT: A  301 TYR cc_start: 0.7644 (m-80) cc_final: 0.7389 (m-80)
REVERT: A  310 LEU cc_start: 0.8981 (pp) cc_final: 0.8520 (tp)
REVERT: C   34 GLU cc_start: 0.8303 (mp0) cc_final: 0.7942 (mp0)
REVERT: C  127 LEU cc_start: 0.9067 (mt) cc_final: 0.8080 (pt)
REVERT: C  310 LEU cc_start: 0.9107 (tp) cc_final: 0.8898 (tt)
REVERT: D   56 ARG cc_start: 0.8002 (ptm-80) cc_final: 0.7609 (ptm160)
REVERT: D   58 TYR cc_start: 0.8518 (t80) cc_final: 0.8217 (t80)
REVERT: D  271 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7401 (m)
REVERT: D  310 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8843 (mt)
  outliers start: 54
  outliers final: 45
  residues processed: 245
  average time/residue: 0.0926
  time to fit residues: 32.5138
Evaluate side-chains
  238 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 190
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   67 ASP
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  226 THR
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   67 ASP
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  295 TRP
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  124 THR
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  212 VAL
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  297 LEU
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   69 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  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
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 129 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 116 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 168 ASN
D 237 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.113028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.086733 restraints weight = 22398.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.089713 restraints weight = 12793.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.091628 restraints weight = 8928.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.092855 restraints weight = 7117.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.093415 restraints weight = 6169.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10672  Z= 0.167
  Angle     :  0.668   8.024  14464  Z= 0.340
  Chirality :  0.043   0.192   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  4.591  20.158   1472
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 20.14 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.23), residues: 1364
  helix:  2.03 (0.19), residues: 680
  sheet: -0.94 (0.33), residues: 208
  loop : -0.37 (0.31), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 303 
 TYR   0.037   0.003   TYR C 222 
 PHE   0.022   0.002   PHE B  79 
 TRP   0.007   0.001   TRP D 147 
 HIS   0.005   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (10672)
  covalent geometry    : angle       0.66785 (14464)
  hydrogen bonds       : bond        0.03677 (  564)
  hydrogen bonds       : angle       4.11698 ( 1608)

*********************** 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
  246 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 198
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7195 (ptm-80)
REVERT: B  271 SER cc_start: 0.7726 (OUTLIER) cc_final: 0.7373 (m)
REVERT: B  292 LEU cc_start: 0.7552 (mm) cc_final: 0.7328 (mp)
REVERT: B  301 TYR cc_start: 0.7858 (m-80) cc_final: 0.7598 (m-80)
REVERT: B  330 ARG cc_start: 0.8306 (mmp-170) cc_final: 0.8074 (mmm160)
REVERT: A  195 ASP cc_start: 0.7291 (t0) cc_final: 0.6955 (m-30)
REVERT: A  206 GLU cc_start: 0.8612 (mm-30) cc_final: 0.7913 (mm-30)
REVERT: A  310 LEU cc_start: 0.8965 (pp) cc_final: 0.8660 (tp)
REVERT: C   79 PHE cc_start: 0.8505 (t80) cc_final: 0.8204 (t80)
REVERT: C  127 LEU cc_start: 0.9063 (mt) cc_final: 0.8099 (pt)
REVERT: C  195 ASP cc_start: 0.7319 (t0) cc_final: 0.7018 (m-30)
REVERT: C  206 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7911 (mm-30)
REVERT: C  283 LEU cc_start: 0.8901 (tp) cc_final: 0.8635 (tp)
REVERT: C  301 TYR cc_start: 0.7736 (m-80) cc_final: 0.7437 (m-80)
REVERT: C  310 LEU cc_start: 0.9088 (tp) cc_final: 0.8857 (pp)
REVERT: D   56 ARG cc_start: 0.7943 (ptm-80) cc_final: 0.7624 (ptm160)
REVERT: D   58 TYR cc_start: 0.8352 (t80) cc_final: 0.7930 (t80)
REVERT: D  100 LYS cc_start: 0.7467 (ptmt) cc_final: 0.7113 (mtmt)
REVERT: D  185 ILE cc_start: 0.9052 (mt) cc_final: 0.8790 (tt)
REVERT: D  271 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7335 (m)
REVERT: D  288 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8276 (tttm)
REVERT: D  310 LEU cc_start: 0.9158 (mt) cc_final: 0.8827 (mt)
  outliers start: 48
  outliers final: 46
  residues processed: 233
  average time/residue: 0.0935
  time to fit residues: 31.0860
Evaluate side-chains
  236 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 188
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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   67 ASP
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  271 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   67 ASP
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  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   67 ASP
Chi-restraints excluded: chain C residue  124 THR
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  185 ILE
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain C residue  305 LEU
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   69 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  157 THR
Chi-restraints excluded: chain D residue  271 SER
Chi-restraints excluded: chain D residue  275 SER
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9980
   chunk 128 optimal weight:    1.9990
   chunk 133 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.114283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.088005 restraints weight = 22493.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.091051 restraints weight = 12771.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.093021 restraints weight = 8872.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.094278 restraints weight = 7034.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.095032 restraints weight = 6072.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10672  Z= 0.140
  Angle     :  0.640   8.261  14464  Z= 0.327
  Chirality :  0.042   0.175   1644
  Planarity :  0.004   0.041   1880
  Dihedral  :  4.394  20.167   1472
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 20.77 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.23), residues: 1364
  helix:  2.00 (0.19), residues: 692
  sheet: -0.89 (0.33), residues: 208
  loop : -0.35 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  42 
 TYR   0.039   0.003   TYR C 222 
 PHE   0.041   0.002   PHE A  79 
 TRP   0.005   0.001   TRP D 147 
 HIS   0.005   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10672)
  covalent geometry    : angle       0.64026 (14464)
  hydrogen bonds       : bond        0.03408 (  564)
  hydrogen bonds       : angle       4.00315 ( 1608)

*********************** 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
  260 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 211
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.8055 (ptm-80) cc_final: 0.7191 (ptm-80)
REVERT: B   60 GLN cc_start: 0.8230 (mt0) cc_final: 0.8029 (mt0)
REVERT: B  127 LEU cc_start: 0.9037 (mt) cc_final: 0.8066 (pt)
REVERT: B  271 SER cc_start: 0.7672 (OUTLIER) cc_final: 0.7295 (m)
REVERT: B  292 LEU cc_start: 0.7560 (mm) cc_final: 0.7339 (mp)
REVERT: B  330 ARG cc_start: 0.8323 (mmp-170) cc_final: 0.8079 (mmm160)
REVERT: A  195 ASP cc_start: 0.7281 (t0) cc_final: 0.6945 (m-30)
REVERT: A  206 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: A  222 TYR cc_start: 0.8728 (t80) cc_final: 0.8150 (t80)
REVERT: A  310 LEU cc_start: 0.8971 (pp) cc_final: 0.8678 (tp)
REVERT: C   30 LEU cc_start: 0.8703 (tt) cc_final: 0.8462 (tp)
REVERT: C  127 LEU cc_start: 0.9032 (mt) cc_final: 0.8066 (pt)
REVERT: C  195 ASP cc_start: 0.7288 (t0) cc_final: 0.7014 (m-30)
REVERT: C  206 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7871 (mm-30)
REVERT: C  283 LEU cc_start: 0.8863 (tp) cc_final: 0.8651 (tp)
REVERT: C  301 TYR cc_start: 0.7654 (m-80) cc_final: 0.7353 (m-80)
REVERT: D  100 LYS cc_start: 0.7361 (ptmt) cc_final: 0.7075 (mtmt)
REVERT: D  168 ASN cc_start: 0.7471 (t0) cc_final: 0.7106 (t0)
REVERT: D  185 ILE cc_start: 0.8991 (mt) cc_final: 0.8725 (tt)
REVERT: D  271 SER cc_start: 0.7661 (OUTLIER) cc_final: 0.7286 (m)
REVERT: D  288 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8279 (tttm)
REVERT: D  310 LEU cc_start: 0.9176 (mt) cc_final: 0.8819 (pp)
  outliers start: 49
  outliers final: 42
  residues processed: 247
  average time/residue: 0.0950
  time to fit residues: 33.4679
Evaluate side-chains
  238 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 194
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   67 ASP
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  271 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain A residue   67 ASP
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  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   67 ASP
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  185 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain C residue  305 LEU
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  306 GLN
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 131 optimal weight:    0.0770
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0870
   chunk 132 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5316

-------------------------------------------------------------------------------
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**
** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 HIS
D 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.116160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.089926 restraints weight = 22055.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.093065 restraints weight = 12406.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.095079 restraints weight = 8554.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.096283 restraints weight = 6761.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.097144 restraints weight = 5863.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4751

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= 0.122
  Angle     :  0.653   8.278  14464  Z= 0.333
  Chirality :  0.041   0.162   1644
  Planarity :  0.004   0.041   1880
  Dihedral  :  4.308  18.972   1472
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 22.48 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.23), residues: 1364
  helix:  1.97 (0.19), residues: 692
  sheet: -0.84 (0.34), residues: 208
  loop : -0.29 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 303 
 TYR   0.040   0.003   TYR C 222 
 PHE   0.035   0.002   PHE C  79 
 TRP   0.013   0.001   TRP D 295 
 HIS   0.005   0.000   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10672)
  covalent geometry    : angle       0.65313 (14464)
  hydrogen bonds       : bond        0.03194 (  564)
  hydrogen bonds       : angle       3.92253 ( 1608)

********************** 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
  252 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 213
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 ARG cc_start: 0.7993 (ptm-80) cc_final: 0.7171 (ptm-80)
REVERT: B   60 GLN cc_start: 0.8222 (mt0) cc_final: 0.8012 (mt0)
REVERT: B  127 LEU cc_start: 0.9014 (mt) cc_final: 0.8057 (pt)
REVERT: B  271 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.7194 (m)
REVERT: B  278 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7776 (pt0)
REVERT: B  292 LEU cc_start: 0.7741 (mm) cc_final: 0.7519 (mp)
REVERT: A  119 ASN cc_start: 0.8605 (t0) cc_final: 0.8326 (t0)
REVERT: A  127 LEU cc_start: 0.8986 (mt) cc_final: 0.8053 (pt)
REVERT: A  195 ASP cc_start: 0.7172 (t0) cc_final: 0.6885 (m-30)
REVERT: A  206 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7816 (mm-30)
REVERT: A  222 TYR cc_start: 0.8684 (t80) cc_final: 0.8263 (t80)
REVERT: A  242 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8121 (tttp)
REVERT: A  310 LEU cc_start: 0.8943 (pp) cc_final: 0.8610 (tp)
REVERT: C  195 ASP cc_start: 0.7193 (t0) cc_final: 0.6830 (m-30)
REVERT: C  283 LEU cc_start: 0.8886 (tp) cc_final: 0.8622 (tp)
REVERT: C  301 TYR cc_start: 0.7466 (m-80) cc_final: 0.7241 (m-80)
REVERT: D   35 SER cc_start: 0.7884 (t) cc_final: 0.7621 (p)
REVERT: D  100 LYS cc_start: 0.7348 (ptmt) cc_final: 0.7065 (mtmt)
REVERT: D  271 SER cc_start: 0.7643 (OUTLIER) cc_final: 0.7290 (m)
  outliers start: 39
  outliers final: 31
  residues processed: 240
  average time/residue: 0.0941
  time to fit residues: 32.2960
Evaluate side-chains
  222 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
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  271 SER
Chi-restraints excluded: chain B residue  310 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  343 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   67 ASP
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  185 ILE
Chi-restraints excluded: chain C residue  252 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  297 LEU
Chi-restraints excluded: chain C residue  343 THR
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  343 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 101 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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**
** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 HIS
** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.115806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.089701 restraints weight = 22122.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.092739 restraints weight = 12517.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.094698 restraints weight = 8687.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.095996 restraints weight = 6889.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.096703 restraints weight = 5929.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4925

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= 0.129
  Angle     :  0.657   8.144  14464  Z= 0.337
  Chirality :  0.042   0.167   1644
  Planarity :  0.004   0.051   1880
  Dihedral  :  4.298  20.638   1472
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.93 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.23), residues: 1364
  helix:  1.90 (0.19), residues: 692
  sheet: -0.81 (0.34), residues: 208
  loop : -0.26 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  42 
 TYR   0.041   0.003   TYR C 222 
 PHE   0.022   0.002   PHE B  79 
 TRP   0.014   0.001   TRP B 295 
 HIS   0.006   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10672)
  covalent geometry    : angle       0.65666 (14464)
  hydrogen bonds       : bond        0.03184 (  564)
  hydrogen bonds       : angle       3.96439 ( 1608)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1656.27 seconds
wall clock time: 29 minutes 35.31 seconds (1775.31 seconds total)