Starting phenix.real_space_refine
on Fri Feb 14 18:51:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ka2_22756/02_2025/7ka2_22756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ka2_22756/02_2025/7ka2_22756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ka2_22756/02_2025/7ka2_22756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ka2_22756/02_2025/7ka2_22756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ka2_22756/02_2025/7ka2_22756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ka2_22756/02_2025/7ka2_22756.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.36, per 1000 atoms: 0.51
  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: 2.54
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      55.7% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  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: 3.22

  Time building geometry restraints manager: 2.95 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2592
        2.78 -     3.31: 9896
        3.31 -     3.84: 18124
        3.84 -     4.37: 21109
        4.37 -     4.90: 35941
  Nonbonded interactions: 87662
  Sorted by model distance:
  nonbonded pdb=" O   MET D 250 "
            pdb=" OG1 THR D 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET B 250 "
            pdb=" OG1 THR B 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   MET C 250 "
            pdb=" OG1 THR C 254 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   THR B  64 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.259 3.040
  ... (remaining 87657 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.630
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
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= 0.525
  Angle     :  0.961   8.127  14464  Z= 0.549
  Chirality :  0.053   0.221   1644
  Planarity :  0.008   0.049   1880
  Dihedral  : 15.204  82.581   3984
  Min Nonbonded Distance : 2.254

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

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

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

*********************** 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
  402 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 334
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  250 MET cc_start: 0.8742 (tpp) cc_final: 0.8428 (tpt)
REVERT: A  233 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.6805 (p)
REVERT: A  250 MET cc_start: 0.8667 (tpp) cc_final: 0.8419 (tpt)
REVERT: A  271 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7989 (p)
REVERT: A  301 TYR cc_start: 0.7412 (m-10) cc_final: 0.7003 (m-10)
REVERT: C   39 ILE cc_start: 0.9263 (tp) cc_final: 0.8931 (tp)
REVERT: C   60 GLN cc_start: 0.8489 (mt0) cc_final: 0.7667 (mt0)
REVERT: C  250 MET cc_start: 0.8731 (tpp) cc_final: 0.8468 (tpt)
REVERT: C  271 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (p)
REVERT: C  301 TYR cc_start: 0.7570 (m-10) cc_final: 0.7022 (m-10)
  outliers start: 68
  outliers final: 6
  residues processed: 373
  average time/residue: 0.2687
  time to fit residues: 133.2938
Evaluate side-chains
  195 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 186
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  271 SER
Chi-restraints excluded: chain D residue   64 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0470
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  60 GLN
B  80 HIS
B 125 GLN
B 168 ASN
A  60 GLN
A  80 HIS
A 125 GLN
A 168 ASN
A 306 GLN
C  60 GLN
C  80 HIS
C 125 GLN
D  80 HIS
D 168 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.095400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.072662 restraints weight = 28987.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.075016 restraints weight = 16885.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.076561 restraints weight = 12007.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2999

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= 0.209
  Angle     :  0.644   8.555  14464  Z= 0.334
  Chirality :  0.043   0.168   1644
  Planarity :  0.004   0.032   1880
  Dihedral  :  4.902  28.077   1481
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 14.75 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.22), residues: 1364
  helix:  0.75 (0.18), residues: 684
  sheet: -1.30 (0.35), residues: 188
  loop : -0.50 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 147 
 HIS   0.003   0.001   HIS B 220 
 PHE   0.015   0.002   PHE B  93 
 TYR   0.019   0.002   TYR C 203 
 ARG   0.004   0.001   ARG D  59 

*********************** 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
  279 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 244
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  165 GLU cc_start: 0.7847 (tp30) cc_final: 0.7339 (tp30)
REVERT: B  311 LYS cc_start: 0.9478 (ttpp) cc_final: 0.9244 (ptmm)
REVERT: B  316 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8739 (mmtm)
REVERT: A   60 GLN cc_start: 0.8888 (mt0) cc_final: 0.8538 (mt0)
REVERT: A   82 THR cc_start: 0.9028 (m) cc_final: 0.8774 (m)
REVERT: C   60 GLN cc_start: 0.8792 (mt0) cc_final: 0.8528 (mt0)
REVERT: C   82 THR cc_start: 0.9066 (m) cc_final: 0.8840 (m)
REVERT: C  250 MET cc_start: 0.8858 (tpp) cc_final: 0.8619 (tpt)
REVERT: C  301 TYR cc_start: 0.7503 (m-10) cc_final: 0.7275 (m-10)
  outliers start: 35
  outliers final: 19
  residues processed: 260
  average time/residue: 0.2267
  time to fit residues: 82.7314
Evaluate side-chains
  181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  226 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 122 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 53 optimal weight:    0.3980
   chunk 2 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0050
   overall best weight:    1.4798

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

Flipped N/Q/H residues before XYZ refinement:
B  80 HIS
B 168 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  80 HIS
A 168 ASN
A 306 GLN
C  80 HIS
C 168 ASN
D 125 GLN
D 168 ASN
D 339 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.092823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.070328 restraints weight = 29965.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.072658 restraints weight = 17341.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.074150 restraints weight = 12190.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  10672  Z= 0.246
  Angle     :  0.627   8.099  14464  Z= 0.325
  Chirality :  0.043   0.158   1644
  Planarity :  0.004   0.063   1880
  Dihedral  :  4.514  20.050   1472
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.92 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.22), residues: 1364
  helix:  1.38 (0.19), residues: 676
  sheet: -0.99 (0.36), residues: 188
  loop : -0.38 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 147 
 HIS   0.011   0.001   HIS A  80 
 PHE   0.018   0.002   PHE B  93 
 TYR   0.016   0.002   TYR B 203 
 ARG   0.005   0.000   ARG D  59 

*********************** 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
  223 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 188
  time to evaluate  : 1.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8384 (p) cc_final: 0.8051 (p)
REVERT: B  229 LYS cc_start: 0.9256 (tttt) cc_final: 0.8803 (tptp)
REVERT: B  250 MET cc_start: 0.8821 (tpt) cc_final: 0.8618 (tpt)
REVERT: A   60 GLN cc_start: 0.8841 (mt0) cc_final: 0.8530 (mt0)
REVERT: A   66 ASP cc_start: 0.9091 (t70) cc_final: 0.8811 (p0)
REVERT: A  301 TYR cc_start: 0.7454 (m-10) cc_final: 0.7202 (m-10)
REVERT: C   34 GLU cc_start: 0.8312 (mp0) cc_final: 0.8085 (mp0)
REVERT: C   60 GLN cc_start: 0.8754 (mt0) cc_final: 0.8485 (mt0)
REVERT: C   66 ASP cc_start: 0.9035 (t70) cc_final: 0.8631 (p0)
REVERT: C   67 ASP cc_start: 0.8970 (p0) cc_final: 0.8736 (t0)
REVERT: C  250 MET cc_start: 0.8829 (tpp) cc_final: 0.8608 (tpt)
REVERT: D  250 MET cc_start: 0.8823 (mmm) cc_final: 0.8481 (tpp)
  outliers start: 35
  outliers final: 22
  residues processed: 212
  average time/residue: 0.2181
  time to fit residues: 66.9863
Evaluate side-chains
  166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  278 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  326 GLU
Chi-restraints excluded: chain D residue  339 GLN
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    0.0980
   chunk 41 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 126 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 125 optimal weight:    0.0020
   chunk 131 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 89 optimal weight:    0.1980
   overall best weight:    0.4188

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.094739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.072366 restraints weight = 29071.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.074748 restraints weight = 16807.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.076235 restraints weight = 11834.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10672  Z= 0.170
  Angle     :  0.612  11.836  14464  Z= 0.308
  Chirality :  0.042   0.170   1644
  Planarity :  0.004   0.050   1880
  Dihedral  :  4.317  18.936   1472
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.81 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.22), residues: 1364
  helix:  1.51 (0.19), residues: 680
  sheet: -0.84 (0.36), residues: 188
  loop : -0.40 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 313 
 HIS   0.009   0.001   HIS C  80 
 PHE   0.014   0.002   PHE C  93 
 TYR   0.020   0.002   TYR B 203 
 ARG   0.005   0.000   ARG D  59 

*********************** 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
  205 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 1.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8358 (p) cc_final: 0.7998 (p)
REVERT: B  229 LYS cc_start: 0.9253 (tttt) cc_final: 0.8790 (tttp)
REVERT: B  311 LYS cc_start: 0.9734 (ptmm) cc_final: 0.9526 (ptmm)
REVERT: A   60 GLN cc_start: 0.8848 (mt0) cc_final: 0.8558 (mt0)
REVERT: A  301 TYR cc_start: 0.7341 (m-10) cc_final: 0.7126 (m-10)
REVERT: A  326 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8561 (tm-30)
REVERT: C   60 GLN cc_start: 0.8766 (mt0) cc_final: 0.8495 (mt0)
REVERT: C  250 MET cc_start: 0.8812 (tpp) cc_final: 0.8599 (tpt)
REVERT: C  330 ARG cc_start: 0.9131 (mmm160) cc_final: 0.8773 (ttp-170)
REVERT: D  250 MET cc_start: 0.8777 (mmm) cc_final: 0.8440 (tpp)
REVERT: D  306 GLN cc_start: 0.7583 (pp30) cc_final: 0.7243 (pp30)
  outliers start: 20
  outliers final: 12
  residues processed: 197
  average time/residue: 0.2378
  time to fit residues: 66.5066
Evaluate side-chains
  169 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 134 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 115 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   overall best weight:    1.1182

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.093579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.071151 restraints weight = 29105.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073487 restraints weight = 16907.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.074962 restraints weight = 11979.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4175

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= 0.206
  Angle     :  0.609  11.547  14464  Z= 0.305
  Chirality :  0.042   0.155   1644
  Planarity :  0.004   0.045   1880
  Dihedral  :  4.167  16.885   1472
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.71 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.22), residues: 1364
  helix:  1.73 (0.19), residues: 684
  sheet: -1.24 (0.32), residues: 220
  loop : -0.30 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 313 
 HIS   0.016   0.001   HIS C  80 
 PHE   0.018   0.001   PHE B  79 
 TYR   0.018   0.002   TYR B 203 
 ARG   0.004   0.000   ARG B 303 

*********************** 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
  201 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8386 (p) cc_final: 0.7977 (p)
REVERT: B  229 LYS cc_start: 0.9310 (tttt) cc_final: 0.8946 (tttt)
REVERT: B  316 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8742 (mmtm)
REVERT: A   60 GLN cc_start: 0.8792 (mt0) cc_final: 0.8528 (mt0)
REVERT: C   60 GLN cc_start: 0.8732 (mt0) cc_final: 0.8475 (mt0)
REVERT: C  250 MET cc_start: 0.8782 (tpp) cc_final: 0.8558 (tpt)
REVERT: C  311 LYS cc_start: 0.9431 (ttpp) cc_final: 0.9228 (ttpp)
REVERT: C  330 ARG cc_start: 0.9142 (mmm160) cc_final: 0.8831 (ttp-170)
REVERT: D  250 MET cc_start: 0.8808 (mmm) cc_final: 0.8483 (tpp)
REVERT: D  306 GLN cc_start: 0.7532 (pp30) cc_final: 0.7298 (pp30)
  outliers start: 29
  outliers final: 18
  residues processed: 188
  average time/residue: 0.2206
  time to fit residues: 58.6559
Evaluate side-chains
  173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 125 optimal weight:    5.9990
   chunk 132 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.7986

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.091904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.069574 restraints weight = 29668.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.071891 restraints weight = 17039.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.073381 restraints weight = 12001.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10672  Z= 0.265
  Angle     :  0.624  11.274  14464  Z= 0.317
  Chirality :  0.043   0.149   1644
  Planarity :  0.004   0.042   1880
  Dihedral  :  4.216  18.541   1472
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.22), residues: 1364
  helix:  1.67 (0.19), residues: 684
  sheet: -0.95 (0.33), residues: 208
  loop : -0.29 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 313 
 HIS   0.010   0.001   HIS A  80 
 PHE   0.020   0.002   PHE B  79 
 TYR   0.021   0.002   TYR B 203 
 ARG   0.005   0.000   ARG B 303 

*********************** 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
  185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8362 (p) cc_final: 0.8003 (p)
REVERT: B  316 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8780 (mmtm)
REVERT: C   60 GLN cc_start: 0.8675 (mt0) cc_final: 0.8412 (mt0)
REVERT: C   66 ASP cc_start: 0.9044 (t0) cc_final: 0.8809 (p0)
REVERT: C   67 ASP cc_start: 0.8956 (p0) cc_final: 0.8749 (t0)
REVERT: C  250 MET cc_start: 0.8774 (tpp) cc_final: 0.8536 (tpt)
REVERT: D  250 MET cc_start: 0.8770 (mmm) cc_final: 0.8522 (tpp)
REVERT: D  306 GLN cc_start: 0.7519 (pp30) cc_final: 0.7310 (pp30)
  outliers start: 27
  outliers final: 21
  residues processed: 176
  average time/residue: 0.2198
  time to fit residues: 55.5924
Evaluate side-chains
  165 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  217 SER
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 109 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 130 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    2.3990

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.090513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.068228 restraints weight = 30250.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.070530 restraints weight = 17173.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.071957 restraints weight = 12037.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.4557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10672  Z= 0.323
  Angle     :  0.656  11.957  14464  Z= 0.332
  Chirality :  0.044   0.151   1644
  Planarity :  0.004   0.040   1880
  Dihedral  :  4.297  19.548   1472
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.06 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.22), residues: 1364
  helix:  1.54 (0.19), residues: 692
  sheet: -0.97 (0.33), residues: 208
  loop : -0.21 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 313 
 HIS   0.014   0.001   HIS B  80 
 PHE   0.022   0.002   PHE B  79 
 TYR   0.023   0.002   TYR B 137 
 ARG   0.004   0.000   ARG B 303 

*********************** 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
  185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 150
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.9101 (t80) cc_final: 0.8881 (t80)
REVERT: B  134 CYS cc_start: 0.8402 (p) cc_final: 0.8029 (p)
REVERT: A  330 ARG cc_start: 0.9147 (mmm160) cc_final: 0.8881 (ttp-170)
REVERT: C   66 ASP cc_start: 0.9077 (t0) cc_final: 0.8850 (p0)
REVERT: C   67 ASP cc_start: 0.8995 (p0) cc_final: 0.8755 (t0)
REVERT: C  250 MET cc_start: 0.8816 (tpp) cc_final: 0.8569 (tpt)
REVERT: D  301 TYR cc_start: 0.7202 (m-80) cc_final: 0.6918 (m-10)
REVERT: D  330 ARG cc_start: 0.9190 (mmm160) cc_final: 0.8799 (ttp-170)
  outliers start: 35
  outliers final: 26
  residues processed: 174
  average time/residue: 0.2250
  time to fit residues: 56.1366
Evaluate side-chains
  165 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   80 HIS
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  217 SER
Chi-restraints excluded: chain D residue  305 LEU
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 10 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   chunk 119 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.3784

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.091530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.069231 restraints weight = 29639.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.071569 restraints weight = 16811.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.073026 restraints weight = 11800.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10672  Z= 0.236
  Angle     :  0.649  12.699  14464  Z= 0.322
  Chirality :  0.043   0.148   1644
  Planarity :  0.004   0.038   1880
  Dihedral  :  4.228  20.488   1472
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.77 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.22), residues: 1364
  helix:  1.65 (0.19), residues: 684
  sheet: -1.02 (0.32), residues: 208
  loop : -0.15 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 313 
 HIS   0.004   0.001   HIS B  80 
 PHE   0.014   0.001   PHE B  79 
 TYR   0.022   0.002   TYR B 137 
 ARG   0.004   0.000   ARG B 303 

*********************** 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
  184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8331 (p) cc_final: 0.7918 (p)
REVERT: B  164 MET cc_start: 0.8648 (tmm) cc_final: 0.8438 (ptt)
REVERT: A  330 ARG cc_start: 0.9126 (mmm160) cc_final: 0.8903 (ttp-170)
REVERT: C   67 ASP cc_start: 0.8931 (p0) cc_final: 0.8727 (t0)
REVERT: C  250 MET cc_start: 0.8791 (tpp) cc_final: 0.8550 (tpt)
REVERT: D  250 MET cc_start: 0.8762 (mmm) cc_final: 0.8510 (tpp)
REVERT: D  301 TYR cc_start: 0.7127 (m-80) cc_final: 0.6849 (m-10)
REVERT: D  330 ARG cc_start: 0.9182 (mmm160) cc_final: 0.8826 (ttp-170)
  outliers start: 28
  outliers final: 19
  residues processed: 176
  average time/residue: 0.2192
  time to fit residues: 55.7624
Evaluate side-chains
  163 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  217 SER
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 94 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 132 optimal weight:    3.9990
   chunk 123 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    1.3588

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.091275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.069660 restraints weight = 30064.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.071963 restraints weight = 17025.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.073434 restraints weight = 11886.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.4805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10672  Z= 0.237
  Angle     :  0.650  12.618  14464  Z= 0.325
  Chirality :  0.043   0.194   1644
  Planarity :  0.004   0.039   1880
  Dihedral  :  4.211  20.152   1472
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.49 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.22), residues: 1364
  helix:  1.67 (0.19), residues: 684
  sheet: -0.99 (0.33), residues: 208
  loop : -0.18 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 313 
 HIS   0.002   0.000   HIS C 245 
 PHE   0.042   0.002   PHE B  79 
 TYR   0.021   0.002   TYR B 137 
 ARG   0.003   0.000   ARG B 303 

*********************** 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
  173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 CYS cc_start: 0.8341 (p) cc_final: 0.7824 (p)
REVERT: B  182 ILE cc_start: 0.8721 (mp) cc_final: 0.8279 (mt)
REVERT: B  301 TYR cc_start: 0.7032 (m-80) cc_final: 0.6704 (m-10)
REVERT: A  330 ARG cc_start: 0.9101 (mmm160) cc_final: 0.8901 (ttm170)
REVERT: C   67 ASP cc_start: 0.8979 (p0) cc_final: 0.8710 (t0)
REVERT: C  250 MET cc_start: 0.8803 (tpp) cc_final: 0.8565 (tpt)
REVERT: D  250 MET cc_start: 0.8754 (mmm) cc_final: 0.8536 (tpp)
REVERT: D  301 TYR cc_start: 0.7081 (m-80) cc_final: 0.6742 (m-10)
REVERT: D  330 ARG cc_start: 0.9166 (mmm160) cc_final: 0.8836 (ttp-170)
  outliers start: 24
  outliers final: 22
  residues processed: 167
  average time/residue: 0.2069
  time to fit residues: 50.9224
Evaluate side-chains
  163 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  217 SER
Chi-restraints excluded: chain B residue  326 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  217 SER
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  217 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 93 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0040
   chunk 9 optimal weight:    0.3980
   chunk 56 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0670
   overall best weight:    0.6732

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.092751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.070815 restraints weight = 29494.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.073173 restraints weight = 16484.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.074640 restraints weight = 11439.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10672  Z= 0.194
  Angle     :  0.649  12.379  14464  Z= 0.324
  Chirality :  0.043   0.164   1644
  Planarity :  0.004   0.046   1880
  Dihedral  :  4.148  20.547   1472
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 21.85 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.22), residues: 1364
  helix:  1.52 (0.19), residues: 708
  sheet: -0.94 (0.33), residues: 208
  loop : -0.14 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 313 
 HIS   0.003   0.001   HIS B  80 
 PHE   0.039   0.002   PHE B  79 
 TYR   0.021   0.002   TYR B 137 
 ARG   0.003   0.000   ARG B 303 

********************** 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
  171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 LEU cc_start: 0.9186 (tp) cc_final: 0.8566 (tt)
REVERT: B  134 CYS cc_start: 0.8350 (p) cc_final: 0.7770 (p)
REVERT: B  182 ILE cc_start: 0.8655 (mp) cc_final: 0.8204 (mt)
REVERT: B  301 TYR cc_start: 0.6940 (m-80) cc_final: 0.6564 (m-10)
REVERT: C   67 ASP cc_start: 0.8963 (p0) cc_final: 0.8701 (t0)
REVERT: C  250 MET cc_start: 0.8771 (tpp) cc_final: 0.8543 (tpt)
REVERT: D  250 MET cc_start: 0.8744 (mmm) cc_final: 0.8527 (tpp)
REVERT: D  301 TYR cc_start: 0.7001 (m-80) cc_final: 0.6680 (m-10)
  outliers start: 20
  outliers final: 16
  residues processed: 164
  average time/residue: 0.1963
  time to fit residues: 47.9541
Evaluate side-chains
  163 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  311 LYS
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   80 HIS
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain D residue   80 HIS
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  252 THR
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 5 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0370
   chunk 58 optimal weight:    0.8980
   chunk 135 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.9864

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.092439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.070546 restraints weight = 29480.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.072869 restraints weight = 16651.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.074310 restraints weight = 11620.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10672  Z= 0.211
  Angle     :  0.658  11.620  14464  Z= 0.328
  Chirality :  0.043   0.148   1644
  Planarity :  0.004   0.048   1880
  Dihedral  :  4.120  20.749   1472
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 22.12 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.23), residues: 1364
  helix:  1.72 (0.19), residues: 684
  sheet: -0.92 (0.33), residues: 208
  loop : -0.20 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 313 
 HIS   0.002   0.000   HIS A 219 
 PHE   0.032   0.002   PHE B  79 
 TYR   0.021   0.002   TYR B 137 
 ARG   0.003   0.000   ARG A 330 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3180.51 seconds
wall clock time: 58 minutes 16.61 seconds (3496.61 seconds total)