Starting phenix.real_space_refine
on Sat Aug 23 04:15:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhc_44540/08_2025/9bhc_44540.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhc_44540/08_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_44540/08_2025/9bhc_44540.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhc_44540/08_2025/9bhc_44540.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhc_44540/08_2025/9bhc_44540.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhc_44540/08_2025/9bhc_44540.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.48, per 1000 atoms: 0.26
  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: 0.94
  Conformation dependent library (CDL) restraints added in 379.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.33
  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: 1.52

  Time building geometry restraints manager: 1.20 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: 0.01
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:             3.130
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.440
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  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:6.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.520
-------------------------------------------------------------------------------
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= 0.940
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.048   0.003   ARG B  76 
 TYR   0.051   0.012   TYR C 294 
 PHE   0.037   0.007   PHE D 121 
 TRP   0.025   0.008   TRP A 265 
 HIS   0.020   0.006   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.01314 ( 9782)
  covalent geometry    : angle       1.19579 (13252)
  hydrogen bonds       : bond        0.13791 (  525)
  hydrogen bonds       : angle       6.21303 ( 1551)

*********************** 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  : 0.392 
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: 0.5346
  time to fit residues: 69.7288
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  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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
B 284 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.087768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.060561 restraints weight = 20759.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 3.45
r_work: 0.2738 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9782  Z= 0.155
  Angle     :  0.602   6.942  13252  Z= 0.299
  Chirality :  0.043   0.144   1558
  Planarity :  0.004   0.039   1686
  Dihedral  :  4.085  25.337   1346
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.80
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.24), residues: 1214
  helix:  2.21 (0.20), residues: 676
  sheet:  0.83 (0.36), residues: 184
  loop : -1.39 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 303 
 TYR   0.023   0.002   TYR D 315 
 PHE   0.033   0.002   PHE D 274 
 TRP   0.017   0.002   TRP D 265 
 HIS   0.002   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9782)
  covalent geometry    : angle       0.60214 (13252)
  hydrogen bonds       : bond        0.04431 (  525)
  hydrogen bonds       : angle       4.58862 ( 1551)

*********************** 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
  125 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9201 (ttpt) cc_final: 0.8569 (tptp)
REVERT: A  220 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8536 (tm)
REVERT: B  258 ARG cc_start: 0.8482 (mtp180) cc_final: 0.8149 (mmm-85)
  outliers start: 14
  outliers final: 2
  residues processed: 119
  average time/residue: 0.5739
  time to fit residues: 73.5333
Evaluate side-chains
  107 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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 90 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 119 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 111 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0670
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.088053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.060938 restraints weight = 20804.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 3.47
r_work: 0.2745 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.1598

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= 0.124
  Angle     :  0.570   7.337  13252  Z= 0.277
  Chirality :  0.042   0.146   1558
  Planarity :  0.004   0.038   1686
  Dihedral  :  3.909  21.101   1346
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.13 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.24), residues: 1214
  helix:  2.35 (0.20), residues: 684
  sheet:  0.90 (0.36), residues: 184
  loop : -1.38 (0.29), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 303 
 TYR   0.023   0.001   TYR B 315 
 PHE   0.039   0.001   PHE D 274 
 TRP   0.014   0.001   TRP D 265 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9782)
  covalent geometry    : angle       0.57012 (13252)
  hydrogen bonds       : bond        0.03711 (  525)
  hydrogen bonds       : angle       4.35081 ( 1551)

*********************** 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
  124 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    8 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8896 (mtmm)
REVERT: C  142 LYS cc_start: 0.9187 (ttpt) cc_final: 0.8582 (tptp)
REVERT: D  257 LEU cc_start: 0.8864 (tt) cc_final: 0.8522 (tm)
REVERT: D  258 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8432 (mmm-85)
REVERT: A    8 LYS cc_start: 0.9117 (mtmm) cc_final: 0.8913 (mtmm)
REVERT: A  220 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8558 (tm)
REVERT: B  257 LEU cc_start: 0.8949 (tt) cc_final: 0.8598 (tm)
REVERT: B  258 ARG cc_start: 0.8463 (mtp180) cc_final: 0.8181 (mmm-85)
REVERT: B  272 MET cc_start: 0.6724 (pmm) cc_final: 0.5847 (mtm)
  outliers start: 14
  outliers final: 6
  residues processed: 118
  average time/residue: 0.5651
  time to fit residues: 71.7625
Evaluate side-chains
  114 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain D residue  222 TYR
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 62 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   chunk 86 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    2.4186

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.084176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.057559 restraints weight = 21129.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 3.40
r_work: 0.2667 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   9782  Z= 0.293
  Angle     :  0.652   6.796  13252  Z= 0.323
  Chirality :  0.047   0.143   1558
  Planarity :  0.005   0.039   1686
  Dihedral  :  4.110  21.775   1346
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.42 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.24), residues: 1214
  helix:  2.29 (0.20), residues: 676
  sheet:  0.55 (0.35), residues: 184
  loop : -1.71 (0.27), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 128 
 TYR   0.020   0.002   TYR D 315 
 PHE   0.028   0.002   PHE D 274 
 TRP   0.008   0.001   TRP D 265 
 HIS   0.003   0.001   HIS D 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00706 ( 9782)
  covalent geometry    : angle       0.65152 (13252)
  hydrogen bonds       : bond        0.04636 (  525)
  hydrogen bonds       : angle       4.52794 ( 1551)

*********************** 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
  135 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8659 (tptp)
REVERT: D  257 LEU cc_start: 0.8855 (tt) cc_final: 0.8645 (tm)
REVERT: D  258 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8511 (mmm-85)
REVERT: D  272 MET cc_start: 0.6938 (pmm) cc_final: 0.6735 (pmm)
REVERT: A  142 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8630 (tptp)
REVERT: A  220 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8570 (tm)
REVERT: B  257 LEU cc_start: 0.8958 (tt) cc_final: 0.8616 (tm)
REVERT: B  258 ARG cc_start: 0.8494 (mtp180) cc_final: 0.8169 (mmm-85)
REVERT: B  272 MET cc_start: 0.6923 (pmm) cc_final: 0.6266 (mtm)
  outliers start: 24
  outliers final: 13
  residues processed: 127
  average time/residue: 0.5421
  time to fit residues: 74.3647
Evaluate side-chains
  121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  242 VAL
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain D residue  222 TYR
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 100 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 119 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.087053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.059929 restraints weight = 20852.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.45
r_work: 0.2718 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9782  Z= 0.124
  Angle     :  0.572   7.835  13252  Z= 0.275
  Chirality :  0.042   0.148   1558
  Planarity :  0.004   0.040   1686
  Dihedral  :  3.915  20.757   1346
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.57 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.24), residues: 1214
  helix:  2.48 (0.20), residues: 684
  sheet:  0.65 (0.37), residues: 180
  loop : -1.57 (0.28), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.023   0.001   TYR B 315 
 PHE   0.033   0.001   PHE B 274 
 TRP   0.007   0.001   TRP D 265 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9782)
  covalent geometry    : angle       0.57227 (13252)
  hydrogen bonds       : bond        0.03586 (  525)
  hydrogen bonds       : angle       4.26377 ( 1551)

*********************** 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
  135 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9174 (ttpt) cc_final: 0.8639 (tptp)
REVERT: D  272 MET cc_start: 0.6759 (pmm) cc_final: 0.6424 (pmm)
REVERT: A  142 LYS cc_start: 0.9156 (ttpt) cc_final: 0.8592 (tptp)
REVERT: A  220 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8616 (tm)
REVERT: B  257 LEU cc_start: 0.8899 (tt) cc_final: 0.8638 (tm)
REVERT: B  258 ARG cc_start: 0.8450 (mtp180) cc_final: 0.8165 (mmm-85)
REVERT: B  272 MET cc_start: 0.6693 (pmm) cc_final: 0.6076 (mtm)
  outliers start: 18
  outliers final: 9
  residues processed: 131
  average time/residue: 0.5476
  time to fit residues: 77.5470
Evaluate side-chains
  116 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain B residue  277 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 112 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 94 optimal weight:    0.2980
   chunk 118 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.085583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.058587 restraints weight = 20735.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 3.46
r_work: 0.2687 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   9782  Z= 0.186
  Angle     :  0.607   7.923  13252  Z= 0.291
  Chirality :  0.044   0.150   1558
  Planarity :  0.004   0.040   1686
  Dihedral  :  3.879  21.076   1346
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.24), residues: 1214
  helix:  2.45 (0.20), residues: 684
  sheet:  0.55 (0.36), residues: 180
  loop : -1.59 (0.28), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 258 
 TYR   0.021   0.002   TYR B 315 
 PHE   0.036   0.001   PHE B 274 
 TRP   0.024   0.001   TRP B 265 
 HIS   0.002   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 9782)
  covalent geometry    : angle       0.60700 (13252)
  hydrogen bonds       : bond        0.03844 (  525)
  hydrogen bonds       : angle       4.29108 ( 1551)

*********************** 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
  126 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8670 (tptp)
REVERT: A    8 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8946 (mtmm)
REVERT: A  142 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8654 (tptp)
REVERT: A  220 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8628 (tm)
REVERT: B  257 LEU cc_start: 0.8931 (tt) cc_final: 0.8660 (tm)
REVERT: B  258 ARG cc_start: 0.8524 (mtp180) cc_final: 0.8208 (mmm-85)
REVERT: B  272 MET cc_start: 0.6715 (pmm) cc_final: 0.6179 (mtm)
  outliers start: 19
  outliers final: 14
  residues processed: 121
  average time/residue: 0.5456
  time to fit residues: 71.2841
Evaluate side-chains
  118 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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  281 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 108 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 105 ASN
D 219 ASN
B 105 ASN
B 219 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.083932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.057079 restraints weight = 21173.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 3.43
r_work: 0.2653 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   9782  Z= 0.310
  Angle     :  0.683   8.073  13252  Z= 0.331
  Chirality :  0.047   0.146   1558
  Planarity :  0.005   0.040   1686
  Dihedral  :  4.047  21.227   1346
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.40 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.24), residues: 1214
  helix:  2.25 (0.20), residues: 682
  sheet:  0.41 (0.36), residues: 180
  loop : -1.70 (0.27), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 258 
 TYR   0.017   0.002   TYR C 294 
 PHE   0.031   0.002   PHE B 274 
 TRP   0.016   0.001   TRP B 265 
 HIS   0.003   0.001   HIS D 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00749 ( 9782)
  covalent geometry    : angle       0.68341 (13252)
  hydrogen bonds       : bond        0.04543 (  525)
  hydrogen bonds       : angle       4.51051 ( 1551)

*********************** 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
  128 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9207 (ttpt) cc_final: 0.8673 (tptp)
REVERT: D  272 MET cc_start: 0.6963 (pmm) cc_final: 0.6033 (mpp)
REVERT: A    8 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8919 (mtmm)
REVERT: A  142 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8729 (tptp)
REVERT: A  220 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8633 (tm)
REVERT: B  257 LEU cc_start: 0.8904 (tt) cc_final: 0.8653 (tm)
REVERT: B  258 ARG cc_start: 0.8477 (mtp180) cc_final: 0.8172 (mmm-85)
REVERT: B  272 MET cc_start: 0.6816 (pmm) cc_final: 0.6390 (mtm)
  outliers start: 23
  outliers final: 18
  residues processed: 121
  average time/residue: 0.5496
  time to fit residues: 71.8391
Evaluate side-chains
  123 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
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  242 VAL
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  281 ILE
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  245 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 88 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 99 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0770
   chunk 83 optimal weight:    6.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.086892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.060205 restraints weight = 20700.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 3.44
r_work: 0.2722 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2248

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= 0.122
  Angle     :  0.602   9.125  13252  Z= 0.284
  Chirality :  0.042   0.145   1558
  Planarity :  0.004   0.042   1686
  Dihedral  :  3.871  19.750   1346
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.68 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.24), residues: 1214
  helix:  2.48 (0.20), residues: 682
  sheet:  0.46 (0.36), residues: 180
  loop : -1.64 (0.28), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 258 
 TYR   0.011   0.001   TYR C 294 
 PHE   0.034   0.001   PHE B 274 
 TRP   0.017   0.001   TRP B 265 
 HIS   0.001   0.000   HIS D 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9782)
  covalent geometry    : angle       0.60223 (13252)
  hydrogen bonds       : bond        0.03475 (  525)
  hydrogen bonds       : angle       4.23673 ( 1551)

*********************** 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
  127 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8683 (tptp)
REVERT: C  259 LEU cc_start: 0.8153 (mp) cc_final: 0.7927 (mm)
REVERT: D  272 MET cc_start: 0.6856 (pmm) cc_final: 0.6059 (mpp)
REVERT: A    8 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8888 (mtmm)
REVERT: A  142 LYS cc_start: 0.9182 (ttpt) cc_final: 0.8707 (tptp)
REVERT: B  257 LEU cc_start: 0.8901 (tt) cc_final: 0.8617 (tm)
REVERT: B  258 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8142 (mmm-85)
REVERT: B  272 MET cc_start: 0.6652 (pmm) cc_final: 0.6243 (mtm)
  outliers start: 20
  outliers final: 13
  residues processed: 124
  average time/residue: 0.5587
  time to fit residues: 74.7323
Evaluate side-chains
  117 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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  281 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  272 MET
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 54 optimal weight:    0.3980
   chunk 68 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.086691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.059630 restraints weight = 20631.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 3.47
r_work: 0.2719 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2290

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= 0.134
  Angle     :  0.609   8.927  13252  Z= 0.286
  Chirality :  0.043   0.147   1558
  Planarity :  0.004   0.040   1686
  Dihedral  :  3.772  19.444   1346
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.07 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.24), residues: 1214
  helix:  2.52 (0.20), residues: 680
  sheet:  0.56 (0.36), residues: 180
  loop : -1.62 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 258 
 TYR   0.023   0.001   TYR B 315 
 PHE   0.035   0.001   PHE B 274 
 TRP   0.015   0.001   TRP B 265 
 HIS   0.002   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9782)
  covalent geometry    : angle       0.60940 (13252)
  hydrogen bonds       : bond        0.03440 (  525)
  hydrogen bonds       : angle       4.19009 ( 1551)

*********************** 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
  121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8686 (tptp)
REVERT: D  272 MET cc_start: 0.6844 (pmm) cc_final: 0.6123 (mpp)
REVERT: A    8 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8919 (mtmm)
REVERT: A  142 LYS cc_start: 0.9183 (ttpt) cc_final: 0.8664 (tptp)
REVERT: B  257 LEU cc_start: 0.8889 (tt) cc_final: 0.8663 (tm)
REVERT: B  258 ARG cc_start: 0.8456 (mtp180) cc_final: 0.8138 (mmm-85)
REVERT: B  272 MET cc_start: 0.6542 (pmm) cc_final: 0.6119 (mtm)
  outliers start: 15
  outliers final: 11
  residues processed: 117
  average time/residue: 0.5936
  time to fit residues: 74.6427
Evaluate side-chains
  113 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
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 D residue  281 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.087573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.060598 restraints weight = 20394.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 3.48
r_work: 0.2737 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9782  Z= 0.120
  Angle     :  0.603   9.040  13252  Z= 0.283
  Chirality :  0.042   0.150   1558
  Planarity :  0.004   0.040   1686
  Dihedral  :  3.727  18.858   1346
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.64 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.24), residues: 1214
  helix:  2.68 (0.20), residues: 666
  sheet:  0.67 (0.36), residues: 180
  loop : -1.57 (0.27), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 258 
 TYR   0.022   0.001   TYR B 315 
 PHE   0.034   0.001   PHE B 274 
 TRP   0.015   0.001   TRP B 265 
 HIS   0.002   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9782)
  covalent geometry    : angle       0.60349 (13252)
  hydrogen bonds       : bond        0.03235 (  525)
  hydrogen bonds       : angle       4.13163 ( 1551)

********************** 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  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  142 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8676 (tptp)
REVERT: D  272 MET cc_start: 0.6813 (pmm) cc_final: 0.6338 (mpp)
REVERT: A    8 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8913 (mtmm)
REVERT: A  142 LYS cc_start: 0.9175 (ttpt) cc_final: 0.8692 (tptp)
REVERT: B  257 LEU cc_start: 0.8894 (tt) cc_final: 0.8679 (tm)
REVERT: B  258 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8089 (mmm-85)
  outliers start: 12
  outliers final: 11
  residues processed: 117
  average time/residue: 0.5614
  time to fit residues: 70.8730
Evaluate side-chains
  119 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  281 ILE
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  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 105 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.085841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.058901 restraints weight = 20781.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 3.48
r_work: 0.2698 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9782  Z= 0.183
  Angle     :  0.628   8.673  13252  Z= 0.297
  Chirality :  0.043   0.146   1558
  Planarity :  0.004   0.039   1686
  Dihedral  :  3.782  17.896   1346
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.24), residues: 1214
  helix:  2.50 (0.20), residues: 678
  sheet:  0.62 (0.36), residues: 180
  loop : -1.60 (0.28), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 258 
 TYR   0.020   0.002   TYR B 315 
 PHE   0.042   0.001   PHE B 274 
 TRP   0.012   0.001   TRP B 265 
 HIS   0.002   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 9782)
  covalent geometry    : angle       0.62776 (13252)
  hydrogen bonds       : bond        0.03693 (  525)
  hydrogen bonds       : angle       4.22695 ( 1551)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3134.49 seconds
wall clock time: 54 minutes 25.49 seconds (3265.49 seconds total)