Starting phenix.real_space_refine
on Wed Apr 30 20:19:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g17_29664/04_2025/8g17_29664.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g17_29664/04_2025/8g17_29664.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g17_29664/04_2025/8g17_29664.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g17_29664/04_2025/8g17_29664.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g17_29664/04_2025/8g17_29664.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g17_29664/04_2025/8g17_29664.cif"
  }
  resolution = 1.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      48      5.16       5
     C    6328      2.51       5
     N    1744      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10016
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2504
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.50, per 1000 atoms: 0.55
  Number of scatterers: 10016
  At special positions: 0
  Unit cell: (99.365, 101.035, 91.015, 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      48     16.00
     O    1896      8.00
     N    1744      7.00
     C    6328      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: 2.63
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 12 sheets defined
      39.2% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 26
    Processing helix  chain 'A' and resid 39 through 49
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 109 through 114'
    Processing helix  chain 'A' and resid 136 through 140
    Processing helix  chain 'A' and resid 151 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 196 through 200
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 317 through 334
    Processing helix  chain 'B' and resid 12 through 26
    Processing helix  chain 'B' and resid 39 through 49
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN B 113 " --> pdb=" O   GLY B 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 109 through 114'
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'B' and resid 151 through 169
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 196 through 200
    Processing helix  chain 'B' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 254 through 268
    Processing helix  chain 'B' and resid 282 through 287
    Processing helix  chain 'B' and resid 317 through 334
    Processing helix  chain 'C' and resid 12 through 26
    Processing helix  chain 'C' and resid 39 through 49
    Processing helix  chain 'C' and resid 81 through 85
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 3.919A  pdb=" N   GLN C 113 " --> pdb=" O   GLY C 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 109 through 114'
    Processing helix  chain 'C' and resid 136 through 140
    Processing helix  chain 'C' and resid 151 through 169
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS C 219 " --> pdb=" O   LYS C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 254 through 268
    Processing helix  chain 'C' and resid 282 through 287
    Processing helix  chain 'C' and resid 317 through 334
    Processing helix  chain 'D' and resid 12 through 26
    Processing helix  chain 'D' and resid 39 through 49
    Processing helix  chain 'D' and resid 81 through 85
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN D 113 " --> pdb=" O   GLY D 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 109 through 114'
    Processing helix  chain 'D' and resid 136 through 140
    Processing helix  chain 'D' and resid 151 through 169
      Proline residue:  D 159  - end of helix
    Processing helix  chain 'D' and resid 196 through 200
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS D 219 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 254 through 268
    Processing helix  chain 'D' and resid 282 through 287
    Processing helix  chain 'D' and resid 317 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP A  29 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   THR A  75 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE A  77 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE A  33 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP B  29 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 9.815A  pdb=" N   THR B  75 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL B  31 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE B  77 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE B  33 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE B  33 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP C  29 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 9.815A  pdb=" N   THR C  75 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL C  31 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE C  77 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE C  33 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL C   8 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.605A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE C 311 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.605A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE C 307 " --> pdb=" O   LEU C 303 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP D  29 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   THR D  75 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL D  31 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE D  77 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE D  33 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE D 311 " --> pdb=" O   ASP D 296 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE D 307 " --> pdb=" O   LEU D 303 " (cutoff:3.500A)

    520 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.24

  Time building geometry restraints manager: 3.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3260
        1.34 -     1.46: 1385
        1.46 -     1.57: 5487
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 10216
  Sorted by residual:
  bond pdb=" N   VAL C 242 "
       pdb=" CA  VAL C 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.11e-02 8.12e+03 1.28e+01
  bond pdb=" N   VAL B 242 "
       pdb=" CA  VAL B 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.11e-02 8.12e+03 1.26e+01
  bond pdb=" N   VAL D 242 "
       pdb=" CA  VAL D 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.11e-02 8.12e+03 1.26e+01
  bond pdb=" N   VAL A 242 "
       pdb=" CA  VAL A 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.11e-02 8.12e+03 1.24e+01
  bond pdb=" N   VAL B 188 "
       pdb=" CA  VAL B 188 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.039 1.15e-02 7.56e+03 1.14e+01
  ... (remaining 10211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 13361
        1.49 -     2.97: 386
        2.97 -     4.46: 73
        4.46 -     5.94: 16
        5.94 -     7.43: 12
  Bond angle restraints: 13848
  Sorted by residual:
  angle pdb=" C   ALA B 150 "
        pdb=" CA  ALA B 150 "
        pdb=" CB  ALA B 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.81    5.82 1.16e+00 7.43e-01 2.52e+01
  angle pdb=" C   ALA D 150 "
        pdb=" CA  ALA D 150 "
        pdb=" CB  ALA D 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.83    5.80 1.16e+00 7.43e-01 2.50e+01
  angle pdb=" C   ALA A 150 "
        pdb=" CA  ALA A 150 "
        pdb=" CB  ALA A 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.83    5.80 1.16e+00 7.43e-01 2.50e+01
  angle pdb=" C   ALA C 150 "
        pdb=" CA  ALA C 150 "
        pdb=" CB  ALA C 150 "
      ideal   model   delta    sigma   weight residual
     116.63  110.88    5.75 1.16e+00 7.43e-01 2.45e+01
  angle pdb=" N   ILE C 206 "
        pdb=" CA  ILE C 206 "
        pdb=" C   ILE C 206 "
      ideal   model   delta    sigma   weight residual
     113.39  107.89    5.50 1.47e+00 4.63e-01 1.40e+01
  ... (remaining 13843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.89: 5408
       16.89 -    33.78: 408
       33.78 -    50.67: 160
       50.67 -    67.56: 60
       67.56 -    84.45: 8
  Dihedral angle restraints: 6044
    sinusoidal: 2268
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CA  ASP A  50 "
           pdb=" CB  ASP A  50 "
           pdb=" CG  ASP A  50 "
           pdb=" OD1 ASP A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.76   54.76     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CA  ASP D  50 "
           pdb=" CB  ASP D  50 "
           pdb=" CG  ASP D  50 "
           pdb=" OD1 ASP D  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.72   54.72     1      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CA  ASP B  50 "
           pdb=" CB  ASP B  50 "
           pdb=" CG  ASP B  50 "
           pdb=" OD1 ASP B  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.69   54.69     1      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 6041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1100
       0.042 -    0.084: 310
       0.084 -    0.127: 146
       0.127 -    0.169: 14
       0.169 -    0.211: 6
  Chirality restraints: 1576
  Sorted by residual:
  chirality pdb=" CA  ILE C 206 "
            pdb=" N   ILE C 206 "
            pdb=" C   ILE C 206 "
            pdb=" CB  ILE C 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE D 206 "
            pdb=" N   ILE D 206 "
            pdb=" C   ILE D 206 "
            pdb=" CB  ILE D 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE A 206 "
            pdb=" N   ILE A 206 "
            pdb=" C   ILE A 206 "
            pdb=" CB  ILE A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 1573 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 207 "   -0.045 5.00e-02 4.00e+02   6.77e-02 7.33e+00
        pdb=" N   PRO D 208 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO D 208 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO D 208 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 207 "   -0.045 5.00e-02 4.00e+02   6.76e-02 7.30e+00
        pdb=" N   PRO C 208 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO C 208 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 208 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 207 "    0.044 5.00e-02 4.00e+02   6.74e-02 7.27e+00
        pdb=" N   PRO B 208 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 208 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 208 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 301
        2.72 -     3.26: 9851
        3.26 -     3.81: 15900
        3.81 -     4.35: 20720
        4.35 -     4.90: 35089
  Nonbonded interactions: 81861
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  94 "
            pdb=" OE2 GLU C 335 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OE2 GLU B 335 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR D  94 "
            pdb=" OE2 GLU D 335 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OE2 GLU A 335 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OE2 GLU C 172 "
            pdb=" NH1 ARG C 248 "
     model   vdw
     2.238 3.120
  ... (remaining 81856 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.090
  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:             0.020
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.070
  Set scattering table:                    0.150
  Process input model:                     25.730
  Find NCS groups from input model:        0.190
  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:             0.010
  Load rotamer database and sin/cos tables:34.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
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      :  0.004   0.041  10216  Z= 0.282
  Angle     :  0.640   7.427  13848  Z= 0.418
  Chirality :  0.049   0.211   1576
  Planarity :  0.005   0.068   1796
  Dihedral  : 15.696  84.451   3636
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 13.64 %
    Favored  : 85.61 %
  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:  0.61 (0.25), residues: 1328
  helix:  1.79 (0.26), residues: 392
  sheet: -0.38 (0.36), residues: 232
  loop : -0.03 (0.27), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 313 
 HIS   0.002   0.001   HIS A  53 
 PHE   0.007   0.001   PHE C 233 
 TYR   0.008   0.001   TYR B 314 
 ARG   0.006   0.001   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18758 (  456)
  hydrogen bonds       : angle       7.15539 ( 1368)
  covalent geometry    : bond        0.00405 (10216)
  covalent geometry    : angle       0.63982 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 170
  time to evaluate  : 1.180 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6871 (m-30) cc_final: 0.6466 (m-30)
REVERT: A   37 PHE cc_start: 0.6293 (m-80) cc_final: 0.5841 (m-80)
REVERT: A   57 HIS cc_start: 0.5836 (m-70) cc_final: 0.5613 (m170)
REVERT: A  130 MET cc_start: 0.7661 (mtm) cc_final: 0.7311 (mtm)
REVERT: A  138 GLU cc_start: 0.6885 (mm-30) cc_final: 0.5028 (pm20)
REVERT: A  141 ASP cc_start: 0.5363 (p0) cc_final: 0.4807 (t0)
REVERT: A  145 LYS cc_start: 0.6942 (mtmt) cc_final: 0.6634 (mmtt)
REVERT: A  223 GLU cc_start: 0.5866 (mp0) cc_final: 0.5389 (mp0)
REVERT: A  239 ASN cc_start: 0.5141 (OUTLIER) cc_final: 0.4854 (t0)
REVERT: A  250 GLU cc_start: 0.6714 (tt0) cc_final: 0.5936 (tp30)
REVERT: A  264 GLN cc_start: 0.6574 (tt0) cc_final: 0.5998 (mt0)
REVERT: A  280 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6736 (mm-40)
REVERT: A  331 MET cc_start: 0.6669 (mtp) cc_final: 0.6316 (mtp)
REVERT: B   29 ASP cc_start: 0.6852 (m-30) cc_final: 0.6456 (m-30)
REVERT: B   37 PHE cc_start: 0.6285 (m-80) cc_final: 0.5813 (m-80)
REVERT: B   57 HIS cc_start: 0.5823 (m-70) cc_final: 0.5607 (m170)
REVERT: B  106 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5393 (tp30)
REVERT: B  130 MET cc_start: 0.7658 (mtm) cc_final: 0.7323 (mtm)
REVERT: B  138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5014 (pm20)
REVERT: B  141 ASP cc_start: 0.5326 (p0) cc_final: 0.4824 (t0)
REVERT: B  145 LYS cc_start: 0.6905 (mtmt) cc_final: 0.6627 (mmtt)
REVERT: B  223 GLU cc_start: 0.5876 (mp0) cc_final: 0.5383 (mp0)
REVERT: B  239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4897 (t0)
REVERT: B  250 GLU cc_start: 0.6646 (tt0) cc_final: 0.5889 (tp30)
REVERT: B  264 GLN cc_start: 0.6524 (tt0) cc_final: 0.5959 (mt0)
REVERT: B  280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6688 (mm-40)
REVERT: B  331 MET cc_start: 0.6676 (mtp) cc_final: 0.6327 (mtp)
REVERT: C   29 ASP cc_start: 0.6849 (m-30) cc_final: 0.6455 (m-30)
REVERT: C   37 PHE cc_start: 0.6276 (m-80) cc_final: 0.5804 (m-80)
REVERT: C   57 HIS cc_start: 0.5819 (m-70) cc_final: 0.5593 (m170)
REVERT: C  106 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5420 (tp30)
REVERT: C  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7322 (mtm)
REVERT: C  138 GLU cc_start: 0.6883 (mm-30) cc_final: 0.5007 (pm20)
REVERT: C  141 ASP cc_start: 0.5344 (p0) cc_final: 0.4828 (t0)
REVERT: C  145 LYS cc_start: 0.6895 (mtmt) cc_final: 0.6619 (mmtt)
REVERT: C  223 GLU cc_start: 0.5862 (mp0) cc_final: 0.5369 (mp0)
REVERT: C  234 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6795 (mtt-85)
REVERT: C  239 ASN cc_start: 0.5158 (OUTLIER) cc_final: 0.4883 (t0)
REVERT: C  250 GLU cc_start: 0.6676 (tt0) cc_final: 0.5936 (tp30)
REVERT: C  264 GLN cc_start: 0.6539 (tt0) cc_final: 0.5974 (mt0)
REVERT: C  280 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6685 (mm-40)
REVERT: C  331 MET cc_start: 0.6664 (mtp) cc_final: 0.6313 (mtp)
REVERT: D   29 ASP cc_start: 0.6869 (m-30) cc_final: 0.6454 (m-30)
REVERT: D   37 PHE cc_start: 0.6305 (m-80) cc_final: 0.5828 (m-80)
REVERT: D   57 HIS cc_start: 0.5835 (m-70) cc_final: 0.5612 (m170)
REVERT: D  106 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5380 (tp30)
REVERT: D  130 MET cc_start: 0.7671 (mtm) cc_final: 0.7318 (mtm)
REVERT: D  138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5019 (pm20)
REVERT: D  141 ASP cc_start: 0.5302 (p0) cc_final: 0.4801 (t0)
REVERT: D  145 LYS cc_start: 0.6869 (mtmt) cc_final: 0.6636 (mmtt)
REVERT: D  223 GLU cc_start: 0.5885 (mp0) cc_final: 0.5400 (mp0)
REVERT: D  239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4901 (t0)
REVERT: D  250 GLU cc_start: 0.6667 (tt0) cc_final: 0.5909 (tp30)
REVERT: D  264 GLN cc_start: 0.6546 (tt0) cc_final: 0.5981 (mt0)
REVERT: D  280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6691 (mm-40)
REVERT: D  331 MET cc_start: 0.6685 (mtp) cc_final: 0.6321 (mtp)
  outliers start: 8
  outliers final: 0
  residues processed: 174
  average time/residue: 1.4800
  time to fit residues: 273.7313
Evaluate side-chains
  132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  239 ASN
Chi-restraints excluded: chain D residue  239 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 77 optimal weight:   20.0000
   chunk 119 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 239 ASN
B 142 ASN
B 239 ASN
C 142 ASN
C 239 ASN
D 142 ASN
D 239 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.153024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.134440 restraints weight = 7167.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 0.64
r_work: 0.3345 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 1.88 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10216  Z= 0.179
  Angle     :  0.653   7.867  13848  Z= 0.365
  Chirality :  0.050   0.241   1576
  Planarity :  0.006   0.060   1796
  Dihedral  :  4.820  19.111   1420
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.26 %
    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:  0.41 (0.25), residues: 1328
  helix:  1.55 (0.26), residues: 392
  sheet: -0.36 (0.38), residues: 204
  loop : -0.17 (0.26), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  87 
 HIS   0.005   0.001   HIS B  53 
 PHE   0.014   0.002   PHE A 233 
 TYR   0.017   0.002   TYR A 314 
 ARG   0.004   0.001   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06378 (  456)
  hydrogen bonds       : angle       5.79316 ( 1368)
  covalent geometry    : bond        0.00321 (10216)
  covalent geometry    : angle       0.65311 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 1.135 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.7723 (m-30) cc_final: 0.7491 (m-30)
REVERT: A  130 MET cc_start: 0.8546 (mtm) cc_final: 0.8337 (mtm)
REVERT: A  138 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7167 (pm20)
REVERT: A  143 SER cc_start: 0.7970 (m) cc_final: 0.7765 (p)
REVERT: A  331 MET cc_start: 0.8082 (mtp) cc_final: 0.7836 (mtp)
REVERT: B   29 ASP cc_start: 0.7726 (m-30) cc_final: 0.7496 (m-30)
REVERT: B  130 MET cc_start: 0.8552 (mtm) cc_final: 0.8343 (mtm)
REVERT: B  138 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7162 (pm20)
REVERT: B  331 MET cc_start: 0.8084 (mtp) cc_final: 0.7844 (mtp)
REVERT: C   29 ASP cc_start: 0.7726 (m-30) cc_final: 0.7497 (m-30)
REVERT: C  130 MET cc_start: 0.8551 (mtm) cc_final: 0.8342 (mtm)
REVERT: C  138 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7155 (pm20)
REVERT: C  331 MET cc_start: 0.8088 (mtp) cc_final: 0.7846 (mtp)
REVERT: D   29 ASP cc_start: 0.7729 (m-30) cc_final: 0.7496 (m-30)
REVERT: D  130 MET cc_start: 0.8547 (mtm) cc_final: 0.8338 (mtm)
REVERT: D  138 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7154 (pm20)
REVERT: D  331 MET cc_start: 0.8085 (mtp) cc_final: 0.7839 (mtp)
  outliers start: 13
  outliers final: 12
  residues processed: 142
  average time/residue: 1.4064
  time to fit residues: 213.0439
Evaluate side-chains
  129 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 98 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 116 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.152781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.133862 restraints weight = 7372.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 0.67
r_work: 0.3327 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work: 0.3057 rms_B_bonded: 4.98 restraints_weight: 0.1250
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10216  Z= 0.164
  Angle     :  0.622   7.421  13848  Z= 0.347
  Chirality :  0.049   0.244   1576
  Planarity :  0.006   0.059   1796
  Dihedral  :  4.752  18.429   1412
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.41 %
    Favored  : 85.32 %
  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:  0.53 (0.24), residues: 1328
  helix:  1.51 (0.26), residues: 392
  sheet: -0.25 (0.39), residues: 176
  loop : -0.04 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  87 
 HIS   0.004   0.001   HIS B  53 
 PHE   0.013   0.002   PHE C 233 
 TYR   0.015   0.002   TYR A 314 
 ARG   0.001   0.000   ARG C  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05908 (  456)
  hydrogen bonds       : angle       5.64370 ( 1368)
  covalent geometry    : bond        0.00292 (10216)
  covalent geometry    : angle       0.62176 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 1.095 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8074 (m-30) cc_final: 0.7845 (m-30)
REVERT: A  138 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7203 (pm20)
REVERT: A  223 GLU cc_start: 0.7767 (mp0) cc_final: 0.7547 (mp0)
REVERT: A  331 MET cc_start: 0.8165 (mtp) cc_final: 0.7872 (mtp)
REVERT: B   29 ASP cc_start: 0.8097 (m-30) cc_final: 0.7875 (m-30)
REVERT: B  138 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7214 (pm20)
REVERT: B  223 GLU cc_start: 0.7734 (mp0) cc_final: 0.7517 (mp0)
REVERT: B  331 MET cc_start: 0.8168 (mtp) cc_final: 0.7879 (mtp)
REVERT: C   29 ASP cc_start: 0.8103 (m-30) cc_final: 0.7879 (m-30)
REVERT: C  138 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7230 (pm20)
REVERT: C  223 GLU cc_start: 0.7751 (mp0) cc_final: 0.7529 (mp0)
REVERT: C  331 MET cc_start: 0.8172 (mtp) cc_final: 0.7885 (mtp)
REVERT: D   29 ASP cc_start: 0.8099 (m-30) cc_final: 0.7876 (m-30)
REVERT: D  138 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7212 (pm20)
REVERT: D  223 GLU cc_start: 0.7737 (mp0) cc_final: 0.7421 (mp0)
REVERT: D  331 MET cc_start: 0.8166 (mtp) cc_final: 0.7874 (mtp)
  outliers start: 24
  outliers final: 16
  residues processed: 137
  average time/residue: 1.4339
  time to fit residues: 208.8048
Evaluate side-chains
  134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 104 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 112 optimal weight:    4.9990
   chunk 66 optimal weight:   20.0000
   chunk 100 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.151846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.133454 restraints weight = 7267.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 0.63
r_work: 0.3335 rms_B_bonded: 1.06 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work: 0.3070 rms_B_bonded: 4.94 restraints_weight: 0.1250
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10216  Z= 0.169
  Angle     :  0.631   7.791  13848  Z= 0.354
  Chirality :  0.049   0.244   1576
  Planarity :  0.006   0.061   1796
  Dihedral  :  4.846  19.024   1412
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 0.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.65 %
    Favored  : 86.08 %
  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:  0.53 (0.24), residues: 1328
  helix:  1.48 (0.26), residues: 392
  sheet: -0.30 (0.39), residues: 176
  loop : -0.02 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  87 
 HIS   0.004   0.001   HIS D  53 
 PHE   0.013   0.002   PHE A 233 
 TYR   0.015   0.002   TYR D 314 
 ARG   0.002   0.000   ARG C  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06023 (  456)
  hydrogen bonds       : angle       5.63124 ( 1368)
  covalent geometry    : bond        0.00302 (10216)
  covalent geometry    : angle       0.63141 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.311 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8084 (m-30) cc_final: 0.7882 (m-30)
REVERT: A  138 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7302 (pm20)
REVERT: A  331 MET cc_start: 0.8268 (mtp) cc_final: 0.7867 (mtp)
REVERT: B  138 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7289 (pm20)
REVERT: B  331 MET cc_start: 0.8265 (mtp) cc_final: 0.7865 (mtp)
REVERT: C  138 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7309 (pm20)
REVERT: C  331 MET cc_start: 0.8263 (mtp) cc_final: 0.7863 (mtp)
REVERT: D  138 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7304 (pm20)
REVERT: D  331 MET cc_start: 0.8266 (mtp) cc_final: 0.7866 (mtp)
  outliers start: 24
  outliers final: 20
  residues processed: 137
  average time/residue: 1.4871
  time to fit residues: 216.9285
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 118 optimal weight:    7.9990
   chunk 103 optimal weight:   20.0000
   chunk 69 optimal weight:    0.8980
   chunk 125 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 99 optimal weight:   20.0000
   chunk 60 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.152738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.134192 restraints weight = 7327.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 0.64
r_work: 0.3354 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 1.87 restraints_weight: 0.2500
r_work: 0.3090 rms_B_bonded: 4.99 restraints_weight: 0.1250
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  10216  Z= 0.143
  Angle     :  0.580   7.235  13848  Z= 0.324
  Chirality :  0.047   0.213   1576
  Planarity :  0.005   0.062   1796
  Dihedral  :  4.725  19.673   1412
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.97 %
    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:  0.51 (0.24), residues: 1328
  helix:  1.58 (0.27), residues: 392
  sheet: -0.09 (0.37), residues: 196
  loop : -0.15 (0.25), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  87 
 HIS   0.003   0.001   HIS B  53 
 PHE   0.013   0.001   PHE D 233 
 TYR   0.014   0.002   TYR D 314 
 ARG   0.001   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05238 (  456)
  hydrogen bonds       : angle       5.44955 ( 1368)
  covalent geometry    : bond        0.00252 (10216)
  covalent geometry    : angle       0.58017 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.230 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8067 (m-30) cc_final: 0.7863 (m-30)
REVERT: A  138 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7307 (pm20)
REVERT: A  223 GLU cc_start: 0.7776 (mp0) cc_final: 0.7475 (mp0)
REVERT: A  331 MET cc_start: 0.8180 (mtp) cc_final: 0.7807 (mtp)
REVERT: B  138 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7295 (pm20)
REVERT: B  223 GLU cc_start: 0.7775 (mp0) cc_final: 0.7481 (mp0)
REVERT: B  250 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7908 (mt-10)
REVERT: B  331 MET cc_start: 0.8178 (mtp) cc_final: 0.7807 (mtp)
REVERT: C  138 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7316 (pm20)
REVERT: C  223 GLU cc_start: 0.7770 (mp0) cc_final: 0.7465 (mp0)
REVERT: C  250 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7877 (mt-10)
REVERT: C  331 MET cc_start: 0.8170 (mtp) cc_final: 0.7795 (mtp)
REVERT: D  138 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7290 (pm20)
REVERT: D  223 GLU cc_start: 0.7765 (mp0) cc_final: 0.7470 (mp0)
REVERT: D  250 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7924 (mt-10)
REVERT: D  331 MET cc_start: 0.8176 (mtp) cc_final: 0.7805 (mtp)
  outliers start: 16
  outliers final: 16
  residues processed: 129
  average time/residue: 1.5118
  time to fit residues: 207.2077
Evaluate side-chains
  133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 93 optimal weight:   20.0000
   chunk 96 optimal weight:    4.9990
   chunk 131 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0030
   chunk 102 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 118 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    2.1596

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.151012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.132162 restraints weight = 7335.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 0.64
r_work: 0.3324 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 1.88 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10216  Z= 0.168
  Angle     :  0.635   8.157  13848  Z= 0.355
  Chirality :  0.049   0.251   1576
  Planarity :  0.006   0.064   1796
  Dihedral  :  4.875  19.988   1412
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.59 %
    Favored  : 85.23 %
  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:  0.49 (0.24), residues: 1328
  helix:  1.47 (0.27), residues: 392
  sheet: -0.29 (0.39), residues: 176
  loop : -0.05 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  87 
 HIS   0.004   0.001   HIS B  53 
 PHE   0.014   0.002   PHE B 233 
 TYR   0.016   0.002   TYR C 314 
 ARG   0.002   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06057 (  456)
  hydrogen bonds       : angle       5.59812 ( 1368)
  covalent geometry    : bond        0.00300 (10216)
  covalent geometry    : angle       0.63541 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 1.120 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7182 (pm20)
REVERT: A  331 MET cc_start: 0.8226 (mtp) cc_final: 0.7847 (mtp)
REVERT: B  138 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7198 (pm20)
REVERT: B  331 MET cc_start: 0.8218 (mtp) cc_final: 0.7843 (mtp)
REVERT: C  138 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7208 (pm20)
REVERT: C  331 MET cc_start: 0.8213 (mtp) cc_final: 0.7837 (mtp)
REVERT: D  138 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7200 (pm20)
REVERT: D  331 MET cc_start: 0.8222 (mtp) cc_final: 0.7847 (mtp)
  outliers start: 23
  outliers final: 21
  residues processed: 135
  average time/residue: 1.4431
  time to fit residues: 207.0755
Evaluate side-chains
  139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   chunk 37 optimal weight:   10.0000
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.150012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.131324 restraints weight = 7332.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 0.63
r_work: 0.3295 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 1.84 restraints_weight: 0.2500
r_work: 0.3028 rms_B_bonded: 4.98 restraints_weight: 0.1250
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10216  Z= 0.211
  Angle     :  0.718   9.402  13848  Z= 0.403
  Chirality :  0.052   0.303   1576
  Planarity :  0.007   0.067   1796
  Dihedral  :  5.105  18.925   1412
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.07 %
    Favored  : 84.85 %
  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:  0.37 (0.24), residues: 1328
  helix:  1.28 (0.26), residues: 392
  sheet: -0.41 (0.39), residues: 176
  loop : -0.06 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP D 313 
 HIS   0.005   0.001   HIS B  53 
 PHE   0.016   0.002   PHE B 233 
 TYR   0.018   0.002   TYR D 314 
 ARG   0.003   0.001   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07133 (  456)
  hydrogen bonds       : angle       5.83272 ( 1368)
  covalent geometry    : bond        0.00391 (10216)
  covalent geometry    : angle       0.71788 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 1.202 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7332 (pm20)
REVERT: A  260 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8405 (ttpp)
REVERT: A  331 MET cc_start: 0.8313 (mtp) cc_final: 0.7974 (mtp)
REVERT: B  138 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7316 (pm20)
REVERT: B  250 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7856 (mt-10)
REVERT: B  260 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8392 (ttpp)
REVERT: B  331 MET cc_start: 0.8310 (mtp) cc_final: 0.7972 (mtp)
REVERT: C  138 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7350 (pm20)
REVERT: C  250 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7866 (mt-10)
REVERT: C  260 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8397 (ttpp)
REVERT: C  331 MET cc_start: 0.8305 (mtp) cc_final: 0.7968 (mtp)
REVERT: D  138 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7313 (pm20)
REVERT: D  250 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7882 (mt-10)
REVERT: D  260 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8392 (ttpp)
REVERT: D  331 MET cc_start: 0.8313 (mtp) cc_final: 0.7976 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 140
  average time/residue: 1.7765
  time to fit residues: 263.5152
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 125 optimal weight:    0.0370
   chunk 38 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   overall best weight:    2.1662

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.151342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.132656 restraints weight = 7346.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 0.64
r_work: 0.3323 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 1.87 restraints_weight: 0.2500
r_work: 0.3060 rms_B_bonded: 4.94 restraints_weight: 0.1250
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10216  Z= 0.170
  Angle     :  0.636   8.642  13848  Z= 0.356
  Chirality :  0.049   0.245   1576
  Planarity :  0.006   0.068   1796
  Dihedral  :  4.961  19.615   1412
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.35 %
    Favored  : 84.56 %
  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:  0.46 (0.24), residues: 1328
  helix:  1.42 (0.26), residues: 392
  sheet: -0.31 (0.39), residues: 176
  loop : -0.06 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  87 
 HIS   0.004   0.001   HIS B  53 
 PHE   0.014   0.002   PHE B 233 
 TYR   0.015   0.002   TYR C 314 
 ARG   0.002   0.000   ARG C  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05999 (  456)
  hydrogen bonds       : angle       5.63398 ( 1368)
  covalent geometry    : bond        0.00304 (10216)
  covalent geometry    : angle       0.63638 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.200 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7322 (pm20)
REVERT: A  260 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8397 (ttpp)
REVERT: A  331 MET cc_start: 0.8280 (mtp) cc_final: 0.7944 (mtp)
REVERT: B  138 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7314 (pm20)
REVERT: B  250 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7828 (mt-10)
REVERT: B  260 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8387 (ttpp)
REVERT: B  331 MET cc_start: 0.8278 (mtp) cc_final: 0.7944 (mtp)
REVERT: C  138 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7333 (pm20)
REVERT: C  250 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7840 (mt-10)
REVERT: C  260 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8396 (ttpp)
REVERT: C  331 MET cc_start: 0.8274 (mtp) cc_final: 0.7939 (mtp)
REVERT: D  138 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7303 (pm20)
REVERT: D  250 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7860 (mt-10)
REVERT: D  260 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8392 (ttpp)
REVERT: D  331 MET cc_start: 0.8278 (mtp) cc_final: 0.7942 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 136
  average time/residue: 1.6160
  time to fit residues: 232.5597
Evaluate side-chains
  138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 92 optimal weight:    0.7980
   chunk 106 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 90 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.151189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.132611 restraints weight = 7285.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 0.63
r_work: 0.3318 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10216  Z= 0.173
  Angle     :  0.652   9.288  13848  Z= 0.365
  Chirality :  0.050   0.257   1576
  Planarity :  0.006   0.067   1796
  Dihedral  :  4.969  19.662   1412
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.64 %
    Favored  : 84.19 %
  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:  0.43 (0.24), residues: 1328
  helix:  1.41 (0.26), residues: 392
  sheet: -0.32 (0.39), residues: 176
  loop : -0.08 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  87 
 HIS   0.004   0.001   HIS D  53 
 PHE   0.014   0.002   PHE B 233 
 TYR   0.016   0.002   TYR D 314 
 ARG   0.002   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06198 (  456)
  hydrogen bonds       : angle       5.65251 ( 1368)
  covalent geometry    : bond        0.00312 (10216)
  covalent geometry    : angle       0.65198 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 1.118 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7234 (pm20)
REVERT: A  260 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8133 (ttpp)
REVERT: A  331 MET cc_start: 0.8249 (mtp) cc_final: 0.7902 (mtp)
REVERT: B  138 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7237 (pm20)
REVERT: B  260 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8134 (ttpp)
REVERT: B  331 MET cc_start: 0.8248 (mtp) cc_final: 0.7903 (mtp)
REVERT: C  138 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7247 (pm20)
REVERT: C  260 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8134 (ttpp)
REVERT: C  331 MET cc_start: 0.8248 (mtp) cc_final: 0.7903 (mtp)
REVERT: D  138 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7231 (pm20)
REVERT: D  260 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8143 (ttpp)
REVERT: D  331 MET cc_start: 0.8250 (mtp) cc_final: 0.7905 (mtp)
  outliers start: 23
  outliers final: 22
  residues processed: 137
  average time/residue: 1.5514
  time to fit residues: 225.2869
Evaluate side-chains
  140 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 122 optimal weight:    0.7980
   chunk 33 optimal weight:   20.0000
   chunk 78 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 119 optimal weight:    9.9990
   chunk 115 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.156056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.138252 restraints weight = 7463.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 0.63
r_work: 0.3386 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 1.86 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10216  Z= 0.121
  Angle     :  0.545   7.125  13848  Z= 0.302
  Chirality :  0.046   0.184   1576
  Planarity :  0.005   0.067   1796
  Dihedral  :  4.638  20.007   1412
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.11 %
    Favored  : 84.09 %
  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:  0.63 (0.24), residues: 1328
  helix:  1.69 (0.27), residues: 392
  sheet: -0.14 (0.39), residues: 176
  loop : -0.05 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  87 
 HIS   0.002   0.000   HIS C  53 
 PHE   0.012   0.001   PHE C 233 
 TYR   0.011   0.001   TYR D 314 
 ARG   0.001   0.000   ARG B 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04531 (  456)
  hydrogen bonds       : angle       5.26694 ( 1368)
  covalent geometry    : bond        0.00213 (10216)
  covalent geometry    : angle       0.54453 (13848)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.168 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7219 (pm20)
REVERT: A  223 GLU cc_start: 0.7436 (mp0) cc_final: 0.7222 (mp0)
REVERT: A  260 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8149 (ttpp)
REVERT: A  331 MET cc_start: 0.8123 (mtp) cc_final: 0.7759 (mtp)
REVERT: B  138 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7226 (pm20)
REVERT: B  223 GLU cc_start: 0.7440 (mp0) cc_final: 0.7233 (mp0)
REVERT: B  260 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8150 (ttpp)
REVERT: B  331 MET cc_start: 0.8121 (mtp) cc_final: 0.7761 (mtp)
REVERT: C  138 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7223 (pm20)
REVERT: C  223 GLU cc_start: 0.7437 (mp0) cc_final: 0.7225 (mp0)
REVERT: C  260 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8149 (ttpp)
REVERT: C  331 MET cc_start: 0.8122 (mtp) cc_final: 0.7760 (mtp)
REVERT: D  138 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7209 (pm20)
REVERT: D  223 GLU cc_start: 0.7440 (mp0) cc_final: 0.7231 (mp0)
REVERT: D  260 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8150 (ttpp)
REVERT: D  331 MET cc_start: 0.8122 (mtp) cc_final: 0.7762 (mtp)
  outliers start: 19
  outliers final: 16
  residues processed: 132
  average time/residue: 1.8006
  time to fit residues: 253.1384
Evaluate side-chains
  128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 118 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 100 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.154977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.137050 restraints weight = 7421.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 0.63
r_work: 0.3400 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work: 0.3147 rms_B_bonded: 4.96 restraints_weight: 0.1250
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10216  Z= 0.130
  Angle     :  0.565   7.697  13848  Z= 0.314
  Chirality :  0.047   0.199   1576
  Planarity :  0.005   0.065   1796
  Dihedral  :  4.644  20.552   1412
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.87 %
    Favored  : 83.43 %
  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:  0.61 (0.24), residues: 1328
  helix:  1.66 (0.27), residues: 392
  sheet: -0.07 (0.39), residues: 176
  loop : -0.08 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  87 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.013   0.001   PHE A 233 
 TYR   0.012   0.001   TYR D 314 
 ARG   0.001   0.000   ARG C  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04848 (  456)
  hydrogen bonds       : angle       5.30822 ( 1368)
  covalent geometry    : bond        0.00231 (10216)
  covalent geometry    : angle       0.56513 (13848)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10605.30 seconds
wall clock time: 184 minutes 23.08 seconds (11063.08 seconds total)