Starting phenix.real_space_refine
on Sat Aug 23 05:04:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g17_29664/08_2025/8g17_29664.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g17_29664/08_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_29664/08_2025/8g17_29664.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g17_29664/08_2025/8g17_29664.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g17_29664/08_2025/8g17_29664.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g17_29664/08_2025/8g17_29664.cif"
  }
  resolution = 1.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D
  Time building chain proxies: 2.06, per 1000 atoms: 0.21
  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: 0.99
  Conformation dependent library (CDL) restraints added in 447.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.54
  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: 1.84

  Time building geometry restraints manager: 1.26 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.740
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.810
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.006   0.001   ARG A 234 
 TYR   0.008   0.001   TYR B 314 
 PHE   0.007   0.001   PHE C 233 
 TRP   0.006   0.001   TRP A 313 
 HIS   0.002   0.001   HIS A  53 

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

*********************** 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  : 0.412 
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: 0.5840 (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: 0.5388 (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: 0.5827 (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: 0.5819 (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: 0.5882 (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: 0.7596
  time to fit residues: 139.7727
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  : 0.451 
-------------------------------------------------------------------------------
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 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0670
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.6124

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.155492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.137276 restraints weight = 7253.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 0.64
r_work: 0.3384 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 1.88 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1304

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= 0.149
  Angle     :  0.594   7.436  13848  Z= 0.331
  Chirality :  0.048   0.197   1576
  Planarity :  0.005   0.058   1796
  Dihedral  :  4.642  22.057   1420
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.55 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.25), residues: 1328
  helix:  1.62 (0.26), residues: 396
  sheet: -0.27 (0.38), residues: 204
  loop : -0.26 (0.25), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 234 
 TYR   0.015   0.002   TYR A 314 
 PHE   0.012   0.001   PHE B 233 
 TRP   0.005   0.001   TRP A  87 
 HIS   0.004   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10216)
  covalent geometry    : angle       0.59428 (13848)
  hydrogen bonds       : bond        0.05548 (  456)
  hydrogen bonds       : angle       5.61958 ( 1368)

*********************** 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
  151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.7705 (m-30) cc_final: 0.7463 (m-30)
REVERT: A  130 MET cc_start: 0.8532 (mtm) cc_final: 0.8249 (mtm)
REVERT: A  138 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7160 (pm20)
REVERT: A  143 SER cc_start: 0.7941 (m) cc_final: 0.7718 (p)
REVERT: B   29 ASP cc_start: 0.7713 (m-30) cc_final: 0.7473 (m-30)
REVERT: B  130 MET cc_start: 0.8542 (mtm) cc_final: 0.8261 (mtm)
REVERT: B  138 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7154 (pm20)
REVERT: B  143 SER cc_start: 0.7967 (m) cc_final: 0.7743 (p)
REVERT: C   29 ASP cc_start: 0.7710 (m-30) cc_final: 0.7473 (m-30)
REVERT: C  130 MET cc_start: 0.8536 (mtm) cc_final: 0.8255 (mtm)
REVERT: C  138 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7158 (pm20)
REVERT: C  143 SER cc_start: 0.7972 (m) cc_final: 0.7743 (p)
REVERT: D   29 ASP cc_start: 0.7696 (m-30) cc_final: 0.7460 (m-30)
REVERT: D  130 MET cc_start: 0.8538 (mtm) cc_final: 0.8254 (mtm)
REVERT: D  138 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7147 (pm20)
REVERT: D  143 SER cc_start: 0.7978 (m) cc_final: 0.7755 (p)
  outliers start: 18
  outliers final: 8
  residues processed: 147
  average time/residue: 0.7026
  time to fit residues: 109.9295
Evaluate side-chains
  131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
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 88 optimal weight:    0.8980
   chunk 81 optimal weight:    0.4980
   chunk 43 optimal weight:   10.0000
   chunk 104 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 83 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 113 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    3.6786

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.149635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.131100 restraints weight = 7324.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 0.63
r_work: 0.3307 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1846

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= 0.221
  Angle     :  0.731   8.410  13848  Z= 0.410
  Chirality :  0.054   0.308   1576
  Planarity :  0.007   0.062   1796
  Dihedral  :  5.010  17.363   1412
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.24), residues: 1328
  helix:  1.30 (0.26), residues: 392
  sheet: -0.42 (0.38), residues: 176
  loop : -0.01 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 248 
 TYR   0.018   0.003   TYR A 314 
 PHE   0.016   0.002   PHE B 233 
 TRP   0.007   0.002   TRP B 313 
 HIS   0.006   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10216)
  covalent geometry    : angle       0.73070 (13848)
  hydrogen bonds       : bond        0.07374 (  456)
  hydrogen bonds       : angle       5.97773 ( 1368)

*********************** 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
  138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7228 (pm20)
REVERT: B  138 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7230 (pm20)
REVERT: C  138 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7233 (pm20)
REVERT: D  138 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7222 (pm20)
  outliers start: 18
  outliers final: 15
  residues processed: 132
  average time/residue: 0.7794
  time to fit residues: 108.9706
Evaluate side-chains
  127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
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  244 ASP
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 126 optimal weight:   20.0000
   chunk 79 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   overall best weight:    2.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.151603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.133346 restraints weight = 7332.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 0.62
r_work: 0.3320 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 1.84 restraints_weight: 0.2500
r_work: 0.3052 rms_B_bonded: 4.94 restraints_weight: 0.1250
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10216  Z= 0.176
  Angle     :  0.643   7.619  13848  Z= 0.360
  Chirality :  0.050   0.252   1576
  Planarity :  0.006   0.064   1796
  Dihedral  :  4.915  18.471   1412
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.27 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.24), residues: 1328
  helix:  1.38 (0.26), residues: 392
  sheet: -0.30 (0.39), residues: 176
  loop : -0.02 (0.24), residues: 760

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10216)
  covalent geometry    : angle       0.64310 (13848)
  hydrogen bonds       : bond        0.06136 (  456)
  hydrogen bonds       : angle       5.69251 ( 1368)

*********************** 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
  138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7316 (pm20)
REVERT: A  223 GLU cc_start: 0.7849 (mp0) cc_final: 0.7647 (mp0)
REVERT: B  138 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7332 (pm20)
REVERT: B  223 GLU cc_start: 0.7845 (mp0) cc_final: 0.7636 (mp0)
REVERT: C  138 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7346 (pm20)
REVERT: C  223 GLU cc_start: 0.7846 (mp0) cc_final: 0.7642 (mp0)
REVERT: D  138 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7313 (pm20)
REVERT: D  223 GLU cc_start: 0.7843 (mp0) cc_final: 0.7637 (mp0)
  outliers start: 20
  outliers final: 16
  residues processed: 134
  average time/residue: 0.7533
  time to fit residues: 107.1308
Evaluate side-chains
  131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 87 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 101 optimal weight:    9.9990
   chunk 61 optimal weight:    9.9990
   chunk 120 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 99 optimal weight:   20.0000
   overall best weight:    3.7986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.149681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.131268 restraints weight = 7255.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 0.62
r_work: 0.3283 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work: 0.3016 rms_B_bonded: 4.94 restraints_weight: 0.1250
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10216  Z= 0.227
  Angle     :  0.748   9.183  13848  Z= 0.420
  Chirality :  0.054   0.315   1576
  Planarity :  0.007   0.065   1796
  Dihedral  :  5.179  18.346   1412
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.93 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.24), residues: 1328
  helix:  1.16 (0.25), residues: 392
  sheet: -0.48 (0.38), residues: 176
  loop : -0.05 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  16 
 TYR   0.018   0.003   TYR D 314 
 PHE   0.017   0.002   PHE D 233 
 TRP   0.007   0.002   TRP B 313 
 HIS   0.006   0.001   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (10216)
  covalent geometry    : angle       0.74788 (13848)
  hydrogen bonds       : bond        0.07510 (  456)
  hydrogen bonds       : angle       5.94008 ( 1368)

*********************** 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
  144 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7349 (pm20)
REVERT: A  260 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8394 (ttpp)
REVERT: B  138 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7341 (pm20)
REVERT: B  223 GLU cc_start: 0.7849 (mp0) cc_final: 0.7647 (mp0)
REVERT: B  260 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8386 (ttpp)
REVERT: C  138 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7350 (pm20)
REVERT: C  260 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8399 (ttpp)
REVERT: D  138 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7341 (pm20)
REVERT: D  260 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8396 (ttpp)
  outliers start: 23
  outliers final: 17
  residues processed: 140
  average time/residue: 0.7777
  time to fit residues: 115.3087
Evaluate side-chains
  133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
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  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 118 optimal weight:    5.9990
   overall best weight:    3.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.150901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.132115 restraints weight = 7280.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 0.64
r_work: 0.3295 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work: 0.3030 rms_B_bonded: 4.92 restraints_weight: 0.1250
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10216  Z= 0.225
  Angle     :  0.743   9.651  13848  Z= 0.417
  Chirality :  0.053   0.301   1576
  Planarity :  0.007   0.068   1796
  Dihedral  :  5.217  18.800   1412
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.24), residues: 1328
  helix:  1.13 (0.25), residues: 392
  sheet: -0.42 (0.39), residues: 176
  loop : -0.08 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  16 
 TYR   0.017   0.003   TYR C 314 
 PHE   0.017   0.002   PHE A 233 
 TRP   0.007   0.002   TRP B 313 
 HIS   0.005   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (10216)
  covalent geometry    : angle       0.74294 (13848)
  hydrogen bonds       : bond        0.07332 (  456)
  hydrogen bonds       : angle       5.94114 ( 1368)

*********************** 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
  150 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   64 ASN cc_start: 0.7512 (m110) cc_final: 0.6983 (t0)
REVERT: A  138 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7329 (pm20)
REVERT: A  260 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8381 (ttpp)
REVERT: B   64 ASN cc_start: 0.7510 (m110) cc_final: 0.6982 (t0)
REVERT: B  138 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7315 (pm20)
REVERT: B  260 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8376 (ttpp)
REVERT: C   64 ASN cc_start: 0.7519 (m110) cc_final: 0.6983 (t0)
REVERT: C  138 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7327 (pm20)
REVERT: C  223 GLU cc_start: 0.7824 (mp0) cc_final: 0.7611 (mp0)
REVERT: C  260 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8381 (ttpp)
REVERT: D   64 ASN cc_start: 0.7500 (m110) cc_final: 0.6979 (t0)
REVERT: D  138 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7324 (pm20)
REVERT: D  223 GLU cc_start: 0.7814 (mp0) cc_final: 0.7607 (mp0)
REVERT: D  260 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8384 (ttpp)
  outliers start: 25
  outliers final: 20
  residues processed: 146
  average time/residue: 0.7265
  time to fit residues: 112.6622
Evaluate side-chains
  140 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 68 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 123 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.152412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.134119 restraints weight = 7359.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 0.63
r_work: 0.3321 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1909

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= 0.166
  Angle     :  0.636   8.646  13848  Z= 0.355
  Chirality :  0.049   0.250   1576
  Planarity :  0.006   0.066   1796
  Dihedral  :  4.989  18.709   1412
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.26 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.24), residues: 1328
  helix:  1.43 (0.26), residues: 392
  sheet: -0.28 (0.39), residues: 176
  loop : -0.07 (0.24), residues: 760

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10216)
  covalent geometry    : angle       0.63623 (13848)
  hydrogen bonds       : bond        0.05888 (  456)
  hydrogen bonds       : angle       5.62535 ( 1368)

*********************** 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
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   64 ASN cc_start: 0.7260 (m110) cc_final: 0.6974 (t0)
REVERT: A  138 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7231 (pm20)
REVERT: A  260 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8147 (ttpp)
REVERT: B   64 ASN cc_start: 0.7254 (m110) cc_final: 0.6982 (t0)
REVERT: B  138 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7234 (pm20)
REVERT: B  260 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8137 (ttpp)
REVERT: C   64 ASN cc_start: 0.7224 (m110) cc_final: 0.6970 (t0)
REVERT: C  138 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7240 (pm20)
REVERT: C  260 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8138 (ttpp)
REVERT: D   64 ASN cc_start: 0.7233 (m110) cc_final: 0.6958 (t0)
REVERT: D  138 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7226 (pm20)
REVERT: D  260 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8140 (ttpp)
  outliers start: 17
  outliers final: 13
  residues processed: 140
  average time/residue: 0.7419
  time to fit residues: 110.1898
Evaluate side-chains
  136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  243 VAL
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  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  243 VAL
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 3 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.153564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.135541 restraints weight = 7361.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 0.62
r_work: 0.3348 rms_B_bonded: 1.05 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 1.82 restraints_weight: 0.2500
r_work: 0.3088 rms_B_bonded: 4.92 restraints_weight: 0.1250
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  10216  Z= 0.146
  Angle     :  0.599   8.286  13848  Z= 0.334
  Chirality :  0.048   0.227   1576
  Planarity :  0.005   0.065   1796
  Dihedral  :  4.857  19.824   1412
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.83 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.24), residues: 1328
  helix:  1.55 (0.26), residues: 392
  sheet: -0.22 (0.38), residues: 176
  loop : -0.05 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  16 
 TYR   0.012   0.002   TYR A 314 
 PHE   0.014   0.001   PHE A 233 
 TRP   0.005   0.001   TRP D  87 
 HIS   0.003   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10216)
  covalent geometry    : angle       0.59912 (13848)
  hydrogen bonds       : bond        0.05336 (  456)
  hydrogen bonds       : angle       5.46967 ( 1368)

*********************** 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
  132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7311 (pm20)
REVERT: A  260 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8415 (ttpp)
REVERT: B  138 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7324 (pm20)
REVERT: B  223 GLU cc_start: 0.7905 (mp0) cc_final: 0.7694 (mp0)
REVERT: B  260 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8403 (ttpp)
REVERT: C  138 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7325 (pm20)
REVERT: C  223 GLU cc_start: 0.7880 (mp0) cc_final: 0.7668 (mp0)
REVERT: C  260 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8407 (ttpp)
REVERT: D  138 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7296 (pm20)
REVERT: D  260 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8415 (ttpp)
  outliers start: 16
  outliers final: 16
  residues processed: 128
  average time/residue: 0.7581
  time to fit residues: 102.9781
Evaluate side-chains
  131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
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  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  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  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  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 22 optimal weight:    4.9990
   chunk 109 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 126 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   chunk 61 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9990
   chunk 6 optimal weight:    8.9990
   chunk 130 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.150791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.131926 restraints weight = 7246.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 0.65
r_work: 0.3288 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 1.84 restraints_weight: 0.2500
r_work: 0.3019 rms_B_bonded: 4.89 restraints_weight: 0.1250
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10216  Z= 0.210
  Angle     :  0.725  10.197  13848  Z= 0.406
  Chirality :  0.052   0.272   1576
  Planarity :  0.007   0.069   1796
  Dihedral  :  5.143  18.820   1412
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.26 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.24), residues: 1328
  helix:  1.31 (0.26), residues: 392
  sheet: -0.36 (0.39), residues: 176
  loop : -0.07 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 323 
 TYR   0.017   0.002   TYR C 314 
 PHE   0.017   0.002   PHE B 233 
 TRP   0.006   0.002   TRP C 313 
 HIS   0.005   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10216)
  covalent geometry    : angle       0.72458 (13848)
  hydrogen bonds       : bond        0.07169 (  456)
  hydrogen bonds       : angle       5.84959 ( 1368)

*********************** 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
  136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7290 (pm20)
REVERT: A  260 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8395 (ttpp)
REVERT: B  138 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7289 (pm20)
REVERT: B  223 GLU cc_start: 0.7845 (mp0) cc_final: 0.7629 (mp0)
REVERT: B  260 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8384 (ttpp)
REVERT: C  138 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7294 (pm20)
REVERT: C  223 GLU cc_start: 0.7824 (mp0) cc_final: 0.7610 (mp0)
REVERT: C  260 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8381 (ttpp)
REVERT: D  138 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7278 (pm20)
REVERT: D  223 GLU cc_start: 0.7874 (mp0) cc_final: 0.7639 (mp0)
REVERT: D  260 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8386 (ttpp)
  outliers start: 21
  outliers final: 13
  residues processed: 132
  average time/residue: 0.7543
  time to fit residues: 105.6886
Evaluate side-chains
  127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
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  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  318 PHE
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 89 optimal weight:    7.9990
   chunk 66 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 88 optimal weight:    8.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    4.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.149698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.130596 restraints weight = 7151.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 0.64
r_work: 0.3264 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 1.84 restraints_weight: 0.2500
r_work: 0.2996 rms_B_bonded: 4.87 restraints_weight: 0.1250
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10216  Z= 0.244
  Angle     :  0.781   9.261  13848  Z= 0.439
  Chirality :  0.053   0.195   1576
  Planarity :  0.008   0.071   1796
  Dihedral  :  5.308  18.886   1412
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.73 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.24), residues: 1328
  helix:  1.12 (0.25), residues: 392
  sheet: -0.45 (0.39), residues: 176
  loop : -0.09 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 323 
 TYR   0.018   0.003   TYR C 314 
 PHE   0.018   0.003   PHE C 233 
 TRP   0.008   0.002   TRP D 313 
 HIS   0.006   0.001   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (10216)
  covalent geometry    : angle       0.78066 (13848)
  hydrogen bonds       : bond        0.07813 (  456)
  hydrogen bonds       : angle       5.99846 ( 1368)

********************** 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
  123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7320 (pm20)
REVERT: A  223 GLU cc_start: 0.7867 (mp0) cc_final: 0.7623 (mp0)
REVERT: A  260 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8403 (ttpp)
REVERT: B  138 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7330 (pm20)
REVERT: B  223 GLU cc_start: 0.7822 (mp0) cc_final: 0.7606 (mp0)
REVERT: B  260 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8395 (ttpp)
REVERT: C  138 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7320 (pm20)
REVERT: C  223 GLU cc_start: 0.7825 (mp0) cc_final: 0.7607 (mp0)
REVERT: C  260 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8394 (ttpp)
REVERT: D  138 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7310 (pm20)
REVERT: D  223 GLU cc_start: 0.7876 (mp0) cc_final: 0.7629 (mp0)
REVERT: D  260 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8399 (ttpp)
  outliers start: 13
  outliers final: 13
  residues processed: 119
  average time/residue: 0.8151
  time to fit residues: 102.5859
Evaluate side-chains
  123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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  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  318 PHE
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 82 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 43 optimal weight:   20.0000
   chunk 32 optimal weight:    4.9990
   chunk 102 optimal weight:   10.0000
   overall best weight:    1.6582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.152249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.133817 restraints weight = 7400.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 0.63
r_work: 0.3326 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 1.86 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  10216  Z= 0.153
  Angle     :  0.611   7.235  13848  Z= 0.342
  Chirality :  0.047   0.137   1576
  Planarity :  0.006   0.069   1796
  Dihedral  :  5.001  19.463   1412
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.02 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.24), residues: 1328
  helix:  1.48 (0.26), residues: 392
  sheet: -0.22 (0.39), residues: 176
  loop : -0.07 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  16 
 TYR   0.013   0.002   TYR D 314 
 PHE   0.014   0.001   PHE C 233 
 TRP   0.005   0.001   TRP D 313 
 HIS   0.003   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10216)
  covalent geometry    : angle       0.61078 (13848)
  hydrogen bonds       : bond        0.05590 (  456)
  hydrogen bonds       : angle       5.53314 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5214.72 seconds
wall clock time: 89 minutes 41.44 seconds (5381.44 seconds total)