Starting phenix.real_space_refine
on Fri Mar 14 06:08:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhc_44540/03_2025/9bhc_44540.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhc_44540/03_2025/9bhc_44540.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bhc_44540/03_2025/9bhc_44540.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhc_44540/03_2025/9bhc_44540.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhc_44540/03_2025/9bhc_44540.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhc_44540/03_2025/9bhc_44540.cif"
  }
  resolution = 2.75
  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=   0.001 sd=   0.011
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      54      5.16       5
     C    6158      2.51       5
     N    1662      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9608
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 2407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2407
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2397
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 13, 'TRANS': 293}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2407
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 13, 'TRANS': 294}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2397
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 13, 'TRANS': 293}
          Chain breaks: 1
  Time building chain proxies: 6.39, per 1000 atoms: 0.67
  Number of scatterers: 9608
  At special positions: 0
  Unit cell: (102.582, 104.25, 100.08, 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      54     16.00
     O    1734      8.00
     N    1662      7.00
     C    6158      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: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2300

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      56.5% alpha, 12.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'C' and resid 22 through 38
      removed outlier: 4.112A  pdb=" N   GLY C  38 " --> pdb=" O   CYS C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 64
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 106 through 108
      No H-bonds generated for 'chain 'C' and resid 106 through 108'
    Processing helix  chain 'C' and resid 109 through 119
    Processing helix  chain 'C' and resid 134 through 153
    Processing helix  chain 'C' and resid 168 through 176
    Processing helix  chain 'C' and resid 183 through 192
      removed outlier: 3.522A  pdb=" N   PHE C 191 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 229
      removed outlier: 4.052A  pdb=" N   THR C 226 " --> pdb=" O   TYR C 222 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   CYS C 227 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 256
      removed outlier: 4.079A  pdb=" N   LEU C 236 " --> pdb=" O   PRO C 232 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE C 243 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER C 251 " --> pdb=" O   GLY C 247 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU C 253 " --> pdb=" O   SER C 249 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE C 255 " --> pdb=" O   SER C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 304
      removed outlier: 3.862A  pdb=" N   PHE C 271 " --> pdb=" O   ALA C 267 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA C 304 " --> pdb=" O   ASN C 300 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 36
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 79 through 89
    Processing helix  chain 'D' and resid 106 through 108
      No H-bonds generated for 'chain 'D' and resid 106 through 108'
    Processing helix  chain 'D' and resid 109 through 119
    Processing helix  chain 'D' and resid 134 through 153
    Processing helix  chain 'D' and resid 168 through 177
    Processing helix  chain 'D' and resid 183 through 192
    Processing helix  chain 'D' and resid 214 through 229
    Processing helix  chain 'D' and resid 230 through 255
      removed outlier: 3.508A  pdb=" N   ARG D 234 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 262
      removed outlier: 3.900A  pdb=" N   ALA D 260 " --> pdb=" O   VAL D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 304
      removed outlier: 3.631A  pdb=" N   THR D 279 " --> pdb=" O   ALA D 275 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE D 280 " --> pdb=" O   VAL D 276 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG D 303 " --> pdb=" O   TYR D 299 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA D 304 " --> pdb=" O   ASN D 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 38
      removed outlier: 4.114A  pdb=" N   GLY A  38 " --> pdb=" O   CYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 79 through 89
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 109 through 119
    Processing helix  chain 'A' and resid 134 through 153
    Processing helix  chain 'A' and resid 168 through 176
    Processing helix  chain 'A' and resid 183 through 192
      removed outlier: 3.522A  pdb=" N   PHE A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 229
      removed outlier: 4.029A  pdb=" N   THR A 226 " --> pdb=" O   TYR A 222 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   CYS A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 256
      removed outlier: 4.088A  pdb=" N   LEU A 236 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 255 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 304
      removed outlier: 3.730A  pdb=" N   PHE A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A 304 " --> pdb=" O   ASN A 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 36
    Processing helix  chain 'B' and resid 53 through 63
    Processing helix  chain 'B' and resid 79 through 89
    Processing helix  chain 'B' and resid 106 through 108
      No H-bonds generated for 'chain 'B' and resid 106 through 108'
    Processing helix  chain 'B' and resid 109 through 119
    Processing helix  chain 'B' and resid 134 through 153
    Processing helix  chain 'B' and resid 168 through 177
    Processing helix  chain 'B' and resid 183 through 192
    Processing helix  chain 'B' and resid 214 through 229
    Processing helix  chain 'B' and resid 230 through 255
    Processing helix  chain 'B' and resid 255 through 262
      removed outlier: 3.871A  pdb=" N   ALA B 260 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 304
      removed outlier: 3.936A  pdb=" N   PHE B 274 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE B 280 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG B 303 " --> pdb=" O   TYR B 299 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA B 304 " --> pdb=" O   ASN B 300 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 195 through 200
      removed outlier: 6.270A  pdb=" N   VAL C 123 " --> pdb=" O   THR C 196 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   ILE C 198 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   GLY C 125 " --> pdb=" O   ILE C 198 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   VAL C 200 " --> pdb=" O   GLY C 125 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL C 127 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   VAL C  10 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   LEU C  44 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL C  12 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ILE C  46 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE C  14 " --> pdb=" O   ILE C  46 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   ASP C  48 " --> pdb=" O   ILE C  14 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   VAL C  16 " --> pdb=" O   ASP C  48 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   ILE C  70 " --> pdb=" O   TRP C  41 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ILE C  43 " --> pdb=" O   ILE C  70 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ILE C  72 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU C  45 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   LEU C  74 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ASP C  47 " --> pdb=" O   LEU C  74 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   SER C  71 " --> pdb=" O   VAL D 313 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   VAL D 313 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU C  73 " --> pdb=" O   GLN D 311 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 310 through 314
      removed outlier: 6.754A  pdb=" N   LEU B  73 " --> pdb=" O   GLN C 311 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   VAL C 313 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   SER B  71 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   ILE B  70 " --> pdb=" O   TRP B  41 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ILE B  43 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ILE B  72 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LEU B  45 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   LEU B  74 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASP B  47 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL B  10 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   LEU B  44 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL B  12 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   ILE B  46 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE B  14 " --> pdb=" O   ILE B  46 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL B 123 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   ILE B 198 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   GLY B 125 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   VAL B 200 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   VAL B 127 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 195 through 200
      removed outlier: 6.249A  pdb=" N   VAL D 123 " --> pdb=" O   THR D 196 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   ILE D 198 " --> pdb=" O   VAL D 123 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   GLY D 125 " --> pdb=" O   ILE D 198 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   VAL D 200 " --> pdb=" O   GLY D 125 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   VAL D 127 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL D  10 " --> pdb=" O   GLU D  42 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU D  44 " --> pdb=" O   VAL D  10 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL D  12 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ILE D  46 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE D  14 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   ILE D  70 " --> pdb=" O   TRP D  41 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ILE D  43 " --> pdb=" O   ILE D  70 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   ILE D  72 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU D  45 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   LEU D  74 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ASP D  47 " --> pdb=" O   LEU D  74 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   SER D  71 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   VAL A 313 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU D  73 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 200
      removed outlier: 6.272A  pdb=" N   VAL A 123 " --> pdb=" O   THR A 196 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   ILE A 198 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   GLY A 125 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   VAL A 200 " --> pdb=" O   GLY A 125 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL A 127 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL A  10 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   LEU A  44 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL A  12 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   ILE A  46 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE A  14 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   ASP A  48 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   VAL A  16 " --> pdb=" O   ASP A  48 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   ILE A  70 " --> pdb=" O   TRP A  41 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ILE A  43 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ILE A  72 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU A  45 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   LEU A  74 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ASP A  47 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   SER A  71 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   VAL B 313 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A  73 " --> pdb=" O   GLN B 311 " (cutoff:3.500A)

    525 hydrogen bonds defined for protein.
    1551 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.69

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1599
        1.31 -     1.45: 2447
        1.45 -     1.58: 5644
        1.58 -     1.72: 0
        1.72 -     1.86: 92
  Bond restraints: 9782
  Sorted by residual:
  bond pdb=" C   PRO C 306 "
       pdb=" O   PRO C 306 "
    ideal  model  delta    sigma   weight residual
    1.233  1.176  0.057 1.16e-02 7.43e+03 2.40e+01
  bond pdb=" C   PRO A 306 "
       pdb=" O   PRO A 306 "
    ideal  model  delta    sigma   weight residual
    1.233  1.177  0.056 1.16e-02 7.43e+03 2.35e+01
  bond pdb=" C   LEU C  74 "
       pdb=" O   LEU C  74 "
    ideal  model  delta    sigma   weight residual
    1.234  1.287 -0.053 1.17e-02 7.31e+03 2.08e+01
  bond pdb=" C   LEU A  74 "
       pdb=" O   LEU A  74 "
    ideal  model  delta    sigma   weight residual
    1.234  1.287 -0.053 1.17e-02 7.31e+03 2.08e+01
  bond pdb=" C   GLY D 153 "
       pdb=" O   GLY D 153 "
    ideal  model  delta    sigma   weight residual
    1.234  1.273 -0.039 9.80e-03 1.04e+04 1.58e+01
  ... (remaining 9777 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 11736
        1.86 -     3.72: 1459
        3.72 -     5.58: 51
        5.58 -     7.45: 4
        7.45 -     9.31: 2
  Bond angle restraints: 13252
  Sorted by residual:
  angle pdb=" C   PHE D 274 "
        pdb=" CA  PHE D 274 "
        pdb=" CB  PHE D 274 "
      ideal   model   delta    sigma   weight residual
     109.29  118.23   -8.94 1.82e+00 3.02e-01 2.41e+01
  angle pdb=" CA  GLY B  79 "
        pdb=" C   GLY B  79 "
        pdb=" O   GLY B  79 "
      ideal   model   delta    sigma   weight residual
     122.22  119.30    2.92 6.50e-01 2.37e+00 2.01e+01
  angle pdb=" CA  GLY D  79 "
        pdb=" C   GLY D  79 "
        pdb=" O   GLY D  79 "
      ideal   model   delta    sigma   weight residual
     122.22  119.42    2.80 6.50e-01 2.37e+00 1.86e+01
  angle pdb=" CA  ASP D  66 "
        pdb=" CB  ASP D  66 "
        pdb=" CG  ASP D  66 "
      ideal   model   delta    sigma   weight residual
     112.60  116.47   -3.87 1.00e+00 1.00e+00 1.50e+01
  angle pdb=" CA  ASP B  66 "
        pdb=" CB  ASP B  66 "
        pdb=" CG  ASP B  66 "
      ideal   model   delta    sigma   weight residual
     112.60  116.47   -3.87 1.00e+00 1.00e+00 1.50e+01
  ... (remaining 13247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 5397
       17.14 -    34.29: 429
       34.29 -    51.43: 70
       51.43 -    68.57: 14
       68.57 -    85.71: 16
  Dihedral angle restraints: 5926
    sinusoidal: 2368
      harmonic: 3558
  Sorted by residual:
  dihedral pdb=" CA  GLY B 269 "
           pdb=" C   GLY B 269 "
           pdb=" N   VAL B 270 "
           pdb=" CA  VAL B 270 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.79  -28.21     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  PHE D 274 "
           pdb=" C   PHE D 274 "
           pdb=" N   ALA D 275 "
           pdb=" CA  ALA D 275 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.87   24.13     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  PHE B 274 "
           pdb=" C   PHE B 274 "
           pdb=" N   ALA B 275 "
           pdb=" CA  ALA B 275 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.97   23.03     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 5923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 738
       0.052 -    0.104: 513
       0.104 -    0.156: 242
       0.156 -    0.208: 59
       0.208 -    0.259: 6
  Chirality restraints: 1558
  Sorted by residual:
  chirality pdb=" CA  PHE D 274 "
            pdb=" N   PHE D 274 "
            pdb=" C   PHE D 274 "
            pdb=" CB  PHE D 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  PHE B 274 "
            pdb=" N   PHE B 274 "
            pdb=" C   PHE B 274 "
            pdb=" CB  PHE B 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CG  LEU B 277 "
            pdb=" CB  LEU B 277 "
            pdb=" CD1 LEU B 277 "
            pdb=" CD2 LEU B 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1555 not shown)

  Planarity restraints: 1686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 294 "   -0.051 2.00e-02 2.50e+03   2.58e-02 1.33e+01
        pdb=" CG  TYR C 294 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 294 "    0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 294 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 294 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 294 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 294 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR C 294 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 294 "    0.050 2.00e-02 2.50e+03   2.56e-02 1.31e+01
        pdb=" CG  TYR A 294 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 294 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 294 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 294 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 294 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 294 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A 294 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 166 "   -0.003 2.00e-02 2.50e+03   2.36e-02 1.11e+01
        pdb=" CG  TYR A 166 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 166 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 166 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 166 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 166 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 166 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A 166 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1683 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 504
        2.74 -     3.28: 10269
        3.28 -     3.82: 15445
        3.82 -     4.36: 19691
        4.36 -     4.90: 32579
  Nonbonded interactions: 78488
  Sorted by model distance:
  nonbonded pdb=" O   THR C 229 "
            pdb=" OH  TYR D 294 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OE1 GLN C  20 "
            pdb=" OG  SER C  53 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OE1 GLN A  20 "
            pdb=" OG  SER A  53 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   THR A 229 "
            pdb=" OH  TYR B 294 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ARG C 234 "
            pdb=" OG  SER C 237 "
     model   vdw
     2.209 3.040
  ... (remaining 78483 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 3 through 317)
  selection = (chain 'B' and (resid 3 through 203 or resid 213 through 317))
  selection = (chain 'C' and resid 3 through 317)
  selection = (chain 'D' and (resid 3 through 203 or resid 213 through 317))
}

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 individual isotropic
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:             3.170
  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:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.480
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.040
  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:13.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
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      :  0.013   0.057   9782  Z= 0.869
  Angle     :  1.196   9.308  13252  Z= 0.861
  Chirality :  0.078   0.259   1558
  Planarity :  0.008   0.045   1686
  Dihedral  : 13.322  85.714   3626
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.24), residues: 1214
  helix:  1.71 (0.20), residues: 674
  sheet:  0.78 (0.37), residues: 180
  loop : -1.41 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.008   TRP A 265 
 HIS   0.020   0.006   HIS B  81 
 PHE   0.037   0.007   PHE D 121 
 TYR   0.051   0.012   TYR C 294 
 ARG   0.048   0.003   ARG B  76 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  258 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.8404 (mtp180)
REVERT: B  272 MET cc_start: 0.6872 (pmm) cc_final: 0.6235 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 1.1179
  time to fit residues: 146.1905
Evaluate side-chains
  100 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 105 ASN
A 105 ASN
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.088053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.060850 restraints weight = 20614.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 3.45
r_work: 0.2743 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9782  Z= 0.222
  Angle     :  0.601   6.886  13252  Z= 0.298
  Chirality :  0.043   0.145   1558
  Planarity :  0.004   0.039   1686
  Dihedral  :  4.071  25.382   1346
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  7.58 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.24), residues: 1214
  helix:  2.22 (0.20), residues: 676
  sheet:  0.87 (0.36), residues: 186
  loop : -1.38 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 265 
 HIS   0.001   0.000   HIS B 201 
 PHE   0.034   0.002   PHE D 274 
 TYR   0.023   0.002   TYR D 315 
 ARG   0.004   0.000   ARG D 258 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9196 (ttpt) cc_final: 0.8566 (tptp)
REVERT: A  220 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8525 (tm)
REVERT: B  258 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8168 (mmm-85)
  outliers start: 14
  outliers final: 2
  residues processed: 120
  average time/residue: 1.0883
  time to fit residues: 141.3514
Evaluate side-chains
  108 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain B residue  218 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 60 optimal weight:    0.3980
   chunk 81 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 119 optimal weight:    0.4980
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 300 ASN
A 300 ASN
B 219 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.085630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.058653 restraints weight = 20987.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.45
r_work: 0.2692 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   9782  Z= 0.329
  Angle     :  0.603   7.098  13252  Z= 0.298
  Chirality :  0.044   0.145   1558
  Planarity :  0.004   0.038   1686
  Dihedral  :  4.016  24.087   1346
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.42 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1214
  helix:  2.37 (0.20), residues: 672
  sheet:  0.69 (0.36), residues: 184
  loop : -1.53 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 265 
 HIS   0.002   0.001   HIS D 202 
 PHE   0.037   0.002   PHE D 274 
 TYR   0.015   0.002   TYR C 294 
 ARG   0.003   0.000   ARG D 303 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    8 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8892 (mtmm)
REVERT: C  142 LYS cc_start: 0.9195 (ttpt) cc_final: 0.8607 (tptp)
REVERT: C  274 PHE cc_start: 0.7616 (t80) cc_final: 0.7408 (t80)
REVERT: D  257 LEU cc_start: 0.8862 (tt) cc_final: 0.8568 (tm)
REVERT: D  258 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8481 (mmm-85)
REVERT: A    8 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8871 (mtmm)
REVERT: A  142 LYS cc_start: 0.9157 (ttpt) cc_final: 0.8565 (tptp)
REVERT: A  220 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8554 (tm)
REVERT: B  257 LEU cc_start: 0.8950 (tt) cc_final: 0.8601 (tm)
REVERT: B  258 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8189 (mmm-85)
REVERT: B  272 MET cc_start: 0.6829 (pmm) cc_final: 0.5999 (mtm)
  outliers start: 15
  outliers final: 6
  residues processed: 121
  average time/residue: 1.1219
  time to fit residues: 146.8445
Evaluate side-chains
  115 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue  288 MET
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0170
   chunk 24 optimal weight:    2.9990
   chunk 115 optimal weight:   40.0000
   chunk 35 optimal weight:    0.9980
   chunk 116 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN
B 219 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.087157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.060188 restraints weight = 20608.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 3.44
r_work: 0.2728 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9782  Z= 0.196
  Angle     :  0.561   7.409  13252  Z= 0.274
  Chirality :  0.042   0.154   1558
  Planarity :  0.004   0.039   1686
  Dihedral  :  3.884  22.538   1346
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.09 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1214
  helix:  2.46 (0.20), residues: 684
  sheet:  0.74 (0.36), residues: 184
  loop : -1.56 (0.29), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 265 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.034   0.001   PHE D 274 
 TYR   0.025   0.001   TYR D 315 
 ARG   0.002   0.000   ARG B 303 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9172 (ttpt) cc_final: 0.8597 (tptp)
REVERT: D  257 LEU cc_start: 0.8853 (tt) cc_final: 0.8599 (tm)
REVERT: D  258 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8499 (mmm-85)
REVERT: A    8 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8925 (mtmm)
REVERT: A  142 LYS cc_start: 0.9143 (ttpt) cc_final: 0.8560 (tptp)
REVERT: A  220 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8590 (tm)
REVERT: B  257 LEU cc_start: 0.8959 (tt) cc_final: 0.8617 (tm)
REVERT: B  258 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8156 (mmm-85)
REVERT: B  272 MET cc_start: 0.6686 (pmm) cc_final: 0.5970 (mtm)
  outliers start: 18
  outliers final: 9
  residues processed: 124
  average time/residue: 1.2180
  time to fit residues: 164.5390
Evaluate side-chains
  119 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  288 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.085797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.058980 restraints weight = 20755.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 3.43
r_work: 0.2695 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9782  Z= 0.313
  Angle     :  0.600   7.679  13252  Z= 0.290
  Chirality :  0.044   0.155   1558
  Planarity :  0.004   0.039   1686
  Dihedral  :  3.877  20.409   1346
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 12.38 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.24), residues: 1214
  helix:  2.48 (0.20), residues: 682
  sheet:  0.70 (0.36), residues: 184
  loop : -1.69 (0.28), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 265 
 HIS   0.002   0.001   HIS B  81 
 PHE   0.037   0.002   PHE D 274 
 TYR   0.020   0.002   TYR B 315 
 ARG   0.002   0.000   ARG C 128 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8646 (tptp)
REVERT: D  273 LEU cc_start: 0.8092 (mt) cc_final: 0.7603 (tt)
REVERT: A  142 LYS cc_start: 0.9162 (ttpt) cc_final: 0.8612 (tptp)
REVERT: A  220 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8612 (tm)
REVERT: B  257 LEU cc_start: 0.8930 (tt) cc_final: 0.8660 (tm)
REVERT: B  258 ARG cc_start: 0.8474 (mtp180) cc_final: 0.8196 (mmm-85)
REVERT: B  272 MET cc_start: 0.6708 (pmm) cc_final: 0.6109 (mtm)
  outliers start: 22
  outliers final: 14
  residues processed: 131
  average time/residue: 1.0200
  time to fit residues: 145.3958
Evaluate side-chains
  121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  127 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   chunk 55 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.085400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.058446 restraints weight = 20860.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 3.43
r_work: 0.2685 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9782  Z= 0.360
  Angle     :  0.620   7.890  13252  Z= 0.300
  Chirality :  0.045   0.147   1558
  Planarity :  0.004   0.040   1686
  Dihedral  :  3.944  20.831   1346
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.53 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1214
  helix:  2.41 (0.20), residues: 684
  sheet:  0.57 (0.36), residues: 180
  loop : -1.67 (0.28), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 265 
 HIS   0.002   0.001   HIS B  81 
 PHE   0.038   0.002   PHE B 274 
 TYR   0.019   0.002   TYR B 315 
 ARG   0.008   0.000   ARG D 258 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.099 
Fit side-chains
REVERT: C  142 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8681 (tptp)
REVERT: D  142 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8572 (mttt)
REVERT: D  273 LEU cc_start: 0.8178 (mt) cc_final: 0.7923 (tp)
REVERT: A    8 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8914 (mtmm)
REVERT: A  142 LYS cc_start: 0.9183 (ttpt) cc_final: 0.8659 (tptp)
REVERT: A  220 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8620 (tm)
REVERT: B  257 LEU cc_start: 0.8945 (tt) cc_final: 0.8663 (tm)
REVERT: B  258 ARG cc_start: 0.8532 (mtp180) cc_final: 0.8225 (mmm-85)
REVERT: B  272 MET cc_start: 0.6771 (pmm) cc_final: 0.6215 (mtm)
  outliers start: 22
  outliers final: 14
  residues processed: 126
  average time/residue: 1.0912
  time to fit residues: 149.3444
Evaluate side-chains
  121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  127 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.086621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.059817 restraints weight = 20889.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.45
r_work: 0.2716 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9782  Z= 0.213
  Angle     :  0.596   8.461  13252  Z= 0.283
  Chirality :  0.043   0.149   1558
  Planarity :  0.004   0.040   1686
  Dihedral  :  3.835  20.020   1346
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.49 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1214
  helix:  2.54 (0.20), residues: 682
  sheet:  0.67 (0.37), residues: 180
  loop : -1.62 (0.28), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 265 
 HIS   0.002   0.000   HIS B  81 
 PHE   0.038   0.001   PHE B 274 
 TYR   0.021   0.001   TYR D 315 
 ARG   0.004   0.000   ARG D 258 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9175 (ttpt) cc_final: 0.8670 (tptp)
REVERT: A    8 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8890 (mtmm)
REVERT: A  142 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8647 (tptp)
REVERT: B  257 LEU cc_start: 0.8900 (tt) cc_final: 0.8687 (tm)
REVERT: B  258 ARG cc_start: 0.8499 (mtp180) cc_final: 0.8218 (mmm-85)
REVERT: B  272 MET cc_start: 0.6641 (pmm) cc_final: 0.6142 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 125
  average time/residue: 1.0383
  time to fit residues: 140.8562
Evaluate side-chains
  119 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  127 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  288 MET
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  288 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 59 optimal weight:    0.0040
   chunk 74 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 117 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.086885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.060280 restraints weight = 20838.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 3.45
r_work: 0.2723 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9782  Z= 0.189
  Angle     :  0.602   8.649  13252  Z= 0.283
  Chirality :  0.043   0.146   1558
  Planarity :  0.004   0.039   1686
  Dihedral  :  3.765  20.484   1346
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.78 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.24), residues: 1214
  helix:  2.57 (0.20), residues: 680
  sheet:  0.73 (0.37), residues: 180
  loop : -1.56 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 265 
 HIS   0.002   0.000   HIS B  81 
 PHE   0.049   0.001   PHE B 274 
 TYR   0.024   0.001   TYR B 315 
 ARG   0.008   0.000   ARG D 258 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9189 (ttpt) cc_final: 0.8664 (tptp)
REVERT: C  259 LEU cc_start: 0.8199 (mp) cc_final: 0.7971 (mm)
REVERT: D  272 MET cc_start: 0.6170 (pmm) cc_final: 0.5945 (pmm)
REVERT: A    8 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8898 (mtmm)
REVERT: A  142 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8651 (tptp)
REVERT: B  257 LEU cc_start: 0.8900 (tt) cc_final: 0.8654 (tm)
REVERT: B  258 ARG cc_start: 0.8506 (mtp180) cc_final: 0.8180 (mmm-85)
REVERT: B  272 MET cc_start: 0.6618 (pmm) cc_final: 0.6144 (mtm)
  outliers start: 18
  outliers final: 14
  residues processed: 118
  average time/residue: 1.0362
  time to fit residues: 132.6453
Evaluate side-chains
  116 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  127 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  288 MET
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 93 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 99 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 110 optimal weight:    0.0870
   chunk 117 optimal weight:    2.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.087321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.060345 restraints weight = 20683.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 3.49
r_work: 0.2732 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9782  Z= 0.188
  Angle     :  0.601   8.801  13252  Z= 0.282
  Chirality :  0.042   0.147   1558
  Planarity :  0.004   0.039   1686
  Dihedral  :  3.735  20.209   1346
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.36 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.24), residues: 1214
  helix:  2.60 (0.20), residues: 680
  sheet:  0.79 (0.37), residues: 180
  loop : -1.52 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 265 
 HIS   0.002   0.000   HIS D  81 
 PHE   0.038   0.001   PHE B 274 
 TYR   0.021   0.001   TYR B 315 
 ARG   0.007   0.000   ARG D 258 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8671 (tptp)
REVERT: A    8 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8884 (mtmm)
REVERT: A  142 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8640 (tptp)
REVERT: B  258 ARG cc_start: 0.8471 (mtp180) cc_final: 0.8176 (mmm-85)
REVERT: B  272 MET cc_start: 0.6487 (pmm) cc_final: 0.6214 (mtm)
  outliers start: 16
  outliers final: 13
  residues processed: 117
  average time/residue: 1.1500
  time to fit residues: 145.2246
Evaluate side-chains
  114 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  127 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  288 MET
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0570
   chunk 51 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0000
   chunk 3 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 90 optimal weight:    0.1980
   chunk 52 optimal weight:    0.0870
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.2280

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.088773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.061777 restraints weight = 20809.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.51
r_work: 0.2756 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9782  Z= 0.152
  Angle     :  0.603   8.829  13252  Z= 0.282
  Chirality :  0.042   0.149   1558
  Planarity :  0.004   0.040   1686
  Dihedral  :  3.657  19.821   1346
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.93 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.25), residues: 1214
  helix:  2.78 (0.21), residues: 668
  sheet:  0.95 (0.38), residues: 180
  loop : -1.45 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 265 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.054   0.001   PHE B 274 
 TYR   0.022   0.001   TYR B 315 
 ARG   0.007   0.000   ARG D 258 

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

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

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2428 Ramachandran restraints generated.
    1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9180 (ttpt) cc_final: 0.8666 (tptp)
REVERT: D  272 MET cc_start: 0.6035 (pmm) cc_final: 0.5725 (pmm)
REVERT: A    1 MET cc_start: 0.8228 (mmm) cc_final: 0.7873 (mmm)
REVERT: A    8 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8875 (mtmm)
REVERT: A  142 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8629 (tptp)
REVERT: B  258 ARG cc_start: 0.8485 (mtp180) cc_final: 0.8169 (mmm-85)
  outliers start: 12
  outliers final: 8
  residues processed: 115
  average time/residue: 1.1188
  time to fit residues: 139.6386
Evaluate side-chains
  113 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  281 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 73 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 116 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.087128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.060206 restraints weight = 20924.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.51
r_work: 0.2725 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9782  Z= 0.216
  Angle     :  0.612   9.001  13252  Z= 0.288
  Chirality :  0.043   0.141   1558
  Planarity :  0.004   0.038   1686
  Dihedral  :  3.656  18.439   1346
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.51 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.24), residues: 1214
  helix:  2.79 (0.21), residues: 668
  sheet:  0.90 (0.37), residues: 180
  loop : -1.48 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 265 
 HIS   0.002   0.001   HIS B  81 
 PHE   0.049   0.001   PHE A 274 
 TYR   0.021   0.001   TYR D 315 
 ARG   0.008   0.000   ARG D 258 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5878.90 seconds
wall clock time: 102 minutes 35.73 seconds (6155.73 seconds total)