Starting phenix.real_space_refine
on Fri Feb 14 06:20:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g17_29664/02_2025/8g17_29664.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g17_29664/02_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_29664/02_2025/8g17_29664.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g17_29664/02_2025/8g17_29664.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g17_29664/02_2025/8g17_29664.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g17_29664/02_2025/8g17_29664.cif"
  }
  resolution = 1.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6328      2.51       5
     N    1744      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10016
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2504
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 4.66, per 1000 atoms: 0.47
  Number of scatterers: 10016
  At special positions: 0
  Unit cell: (99.365, 101.035, 91.015, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1896      8.00
     N    1744      7.00
     C    6328      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 12 sheets defined
      39.2% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 26
    Processing helix  chain 'A' and resid 39 through 49
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 109 through 114'
    Processing helix  chain 'A' and resid 136 through 140
    Processing helix  chain 'A' and resid 151 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 196 through 200
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 317 through 334
    Processing helix  chain 'B' and resid 12 through 26
    Processing helix  chain 'B' and resid 39 through 49
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN B 113 " --> pdb=" O   GLY B 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 109 through 114'
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'B' and resid 151 through 169
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 196 through 200
    Processing helix  chain 'B' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 254 through 268
    Processing helix  chain 'B' and resid 282 through 287
    Processing helix  chain 'B' and resid 317 through 334
    Processing helix  chain 'C' and resid 12 through 26
    Processing helix  chain 'C' and resid 39 through 49
    Processing helix  chain 'C' and resid 81 through 85
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 3.919A  pdb=" N   GLN C 113 " --> pdb=" O   GLY C 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 109 through 114'
    Processing helix  chain 'C' and resid 136 through 140
    Processing helix  chain 'C' and resid 151 through 169
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS C 219 " --> pdb=" O   LYS C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 254 through 268
    Processing helix  chain 'C' and resid 282 through 287
    Processing helix  chain 'C' and resid 317 through 334
    Processing helix  chain 'D' and resid 12 through 26
    Processing helix  chain 'D' and resid 39 through 49
    Processing helix  chain 'D' and resid 81 through 85
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 109 through 114
      removed outlier: 3.918A  pdb=" N   GLN D 113 " --> pdb=" O   GLY D 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 109 through 114'
    Processing helix  chain 'D' and resid 136 through 140
    Processing helix  chain 'D' and resid 151 through 169
      Proline residue:  D 159  - end of helix
    Processing helix  chain 'D' and resid 196 through 200
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 3.816A  pdb=" N   GLY D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS D 219 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 254 through 268
    Processing helix  chain 'D' and resid 282 through 287
    Processing helix  chain 'D' and resid 317 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP A  29 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   THR A  75 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE A  77 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE A  33 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLY A 173 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 246 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET A 175 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP A 244 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR A 177 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP B  29 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 9.815A  pdb=" N   THR B  75 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL B  31 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE B  77 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE B  33 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE B  33 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG B 248 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY B 173 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR B 246 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET B 175 " --> pdb=" O   ASP B 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP B 244 " --> pdb=" O   MET B 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP C  29 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 9.815A  pdb=" N   THR C  75 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL C  31 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE C  77 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE C  33 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL C   8 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.605A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE C 311 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.605A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG C 248 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY C 173 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR C 246 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET C 175 " --> pdb=" O   ASP C 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP C 244 " --> pdb=" O   MET C 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR C 177 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL C 242 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE C 307 " --> pdb=" O   LEU C 303 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63
      removed outlier: 10.277A  pdb=" N   ASP D  29 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   THR D  75 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL D  31 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   PHE D  77 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE D  33 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ILE D 311 " --> pdb=" O   ASP D 296 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.604A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ARG D 248 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLY D 173 " --> pdb=" O   THR D 246 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR D 246 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET D 175 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASP D 244 " --> pdb=" O   MET D 175 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   THR D 177 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D 242 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE D 307 " --> pdb=" O   LEU D 303 " (cutoff:3.500A)

    520 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.31

  Time building geometry restraints manager: 2.87 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.190
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.050
-------------------------------------------------------------------------------
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= 0.272
  Angle     :  0.640   7.427  13848  Z= 0.418
  Chirality :  0.049   0.211   1576
  Planarity :  0.005   0.068   1796
  Dihedral  : 15.696  84.451   3636
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 13.64 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1328
  helix:  1.79 (0.26), residues: 392
  sheet: -0.38 (0.36), residues: 232
  loop : -0.03 (0.27), residues: 704

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

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

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 170
  time to evaluate  : 1.146 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.6871 (m-30) cc_final: 0.6466 (m-30)
REVERT: A   37 PHE cc_start: 0.6293 (m-80) cc_final: 0.5841 (m-80)
REVERT: A   57 HIS cc_start: 0.5836 (m-70) cc_final: 0.5613 (m170)
REVERT: A  130 MET cc_start: 0.7661 (mtm) cc_final: 0.7311 (mtm)
REVERT: A  138 GLU cc_start: 0.6885 (mm-30) cc_final: 0.5028 (pm20)
REVERT: A  141 ASP cc_start: 0.5363 (p0) cc_final: 0.4807 (t0)
REVERT: A  145 LYS cc_start: 0.6942 (mtmt) cc_final: 0.6634 (mmtt)
REVERT: A  223 GLU cc_start: 0.5866 (mp0) cc_final: 0.5389 (mp0)
REVERT: A  239 ASN cc_start: 0.5141 (OUTLIER) cc_final: 0.4854 (t0)
REVERT: A  250 GLU cc_start: 0.6714 (tt0) cc_final: 0.5936 (tp30)
REVERT: A  264 GLN cc_start: 0.6574 (tt0) cc_final: 0.5998 (mt0)
REVERT: A  280 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6736 (mm-40)
REVERT: A  331 MET cc_start: 0.6669 (mtp) cc_final: 0.6316 (mtp)
REVERT: B   29 ASP cc_start: 0.6852 (m-30) cc_final: 0.6456 (m-30)
REVERT: B   37 PHE cc_start: 0.6285 (m-80) cc_final: 0.5813 (m-80)
REVERT: B   57 HIS cc_start: 0.5823 (m-70) cc_final: 0.5607 (m170)
REVERT: B  106 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5393 (tp30)
REVERT: B  130 MET cc_start: 0.7658 (mtm) cc_final: 0.7323 (mtm)
REVERT: B  138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5014 (pm20)
REVERT: B  141 ASP cc_start: 0.5326 (p0) cc_final: 0.4824 (t0)
REVERT: B  145 LYS cc_start: 0.6905 (mtmt) cc_final: 0.6627 (mmtt)
REVERT: B  223 GLU cc_start: 0.5876 (mp0) cc_final: 0.5383 (mp0)
REVERT: B  239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4897 (t0)
REVERT: B  250 GLU cc_start: 0.6646 (tt0) cc_final: 0.5889 (tp30)
REVERT: B  264 GLN cc_start: 0.6524 (tt0) cc_final: 0.5959 (mt0)
REVERT: B  280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6688 (mm-40)
REVERT: B  331 MET cc_start: 0.6676 (mtp) cc_final: 0.6327 (mtp)
REVERT: C   29 ASP cc_start: 0.6849 (m-30) cc_final: 0.6455 (m-30)
REVERT: C   37 PHE cc_start: 0.6276 (m-80) cc_final: 0.5804 (m-80)
REVERT: C   57 HIS cc_start: 0.5819 (m-70) cc_final: 0.5593 (m170)
REVERT: C  106 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5420 (tp30)
REVERT: C  130 MET cc_start: 0.7657 (mtm) cc_final: 0.7322 (mtm)
REVERT: C  138 GLU cc_start: 0.6883 (mm-30) cc_final: 0.5007 (pm20)
REVERT: C  141 ASP cc_start: 0.5344 (p0) cc_final: 0.4828 (t0)
REVERT: C  145 LYS cc_start: 0.6895 (mtmt) cc_final: 0.6619 (mmtt)
REVERT: C  223 GLU cc_start: 0.5862 (mp0) cc_final: 0.5369 (mp0)
REVERT: C  234 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6795 (mtt-85)
REVERT: C  239 ASN cc_start: 0.5158 (OUTLIER) cc_final: 0.4883 (t0)
REVERT: C  250 GLU cc_start: 0.6676 (tt0) cc_final: 0.5936 (tp30)
REVERT: C  264 GLN cc_start: 0.6539 (tt0) cc_final: 0.5974 (mt0)
REVERT: C  280 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6685 (mm-40)
REVERT: C  331 MET cc_start: 0.6664 (mtp) cc_final: 0.6313 (mtp)
REVERT: D   29 ASP cc_start: 0.6869 (m-30) cc_final: 0.6454 (m-30)
REVERT: D   37 PHE cc_start: 0.6305 (m-80) cc_final: 0.5828 (m-80)
REVERT: D   57 HIS cc_start: 0.5835 (m-70) cc_final: 0.5612 (m170)
REVERT: D  106 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5380 (tp30)
REVERT: D  130 MET cc_start: 0.7671 (mtm) cc_final: 0.7318 (mtm)
REVERT: D  138 GLU cc_start: 0.6884 (mm-30) cc_final: 0.5019 (pm20)
REVERT: D  141 ASP cc_start: 0.5302 (p0) cc_final: 0.4801 (t0)
REVERT: D  145 LYS cc_start: 0.6869 (mtmt) cc_final: 0.6636 (mmtt)
REVERT: D  223 GLU cc_start: 0.5885 (mp0) cc_final: 0.5400 (mp0)
REVERT: D  239 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4901 (t0)
REVERT: D  250 GLU cc_start: 0.6667 (tt0) cc_final: 0.5909 (tp30)
REVERT: D  264 GLN cc_start: 0.6546 (tt0) cc_final: 0.5981 (mt0)
REVERT: D  280 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6691 (mm-40)
REVERT: D  331 MET cc_start: 0.6685 (mtp) cc_final: 0.6321 (mtp)
  outliers start: 8
  outliers final: 0
  residues processed: 174
  average time/residue: 1.5459
  time to fit residues: 284.6624
Evaluate side-chains
  132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  239 ASN
Chi-restraints excluded: chain D residue  239 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 77 optimal weight:   20.0000
   chunk 119 optimal weight:    3.9990
   overall best weight:    2.3988

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.153024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.134439 restraints weight = 7167.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 0.64
r_work: 0.3344 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 1.86 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10216  Z= 0.214
  Angle     :  0.653   7.867  13848  Z= 0.365
  Chirality :  0.050   0.241   1576
  Planarity :  0.006   0.060   1796
  Dihedral  :  4.820  19.111   1420
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.26 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1328
  helix:  1.55 (0.26), residues: 392
  sheet: -0.36 (0.38), residues: 204
  loop : -0.17 (0.26), residues: 732

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

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

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.7725 (m-30) cc_final: 0.7496 (m-30)
REVERT: A  130 MET cc_start: 0.8538 (mtm) cc_final: 0.8330 (mtm)
REVERT: A  138 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7182 (pm20)
REVERT: A  331 MET cc_start: 0.8092 (mtp) cc_final: 0.7851 (mtp)
REVERT: B   29 ASP cc_start: 0.7729 (m-30) cc_final: 0.7503 (m-30)
REVERT: B  130 MET cc_start: 0.8547 (mtm) cc_final: 0.8338 (mtm)
REVERT: B  138 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7179 (pm20)
REVERT: B  331 MET cc_start: 0.8094 (mtp) cc_final: 0.7857 (mtp)
REVERT: C   29 ASP cc_start: 0.7730 (m-30) cc_final: 0.7506 (m-30)
REVERT: C  130 MET cc_start: 0.8547 (mtm) cc_final: 0.8339 (mtm)
REVERT: C  138 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7170 (pm20)
REVERT: C  331 MET cc_start: 0.8099 (mtp) cc_final: 0.7861 (mtp)
REVERT: D   29 ASP cc_start: 0.7729 (m-30) cc_final: 0.7502 (m-30)
REVERT: D  130 MET cc_start: 0.8542 (mtm) cc_final: 0.8331 (mtm)
REVERT: D  138 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7171 (pm20)
REVERT: D  331 MET cc_start: 0.8095 (mtp) cc_final: 0.7853 (mtp)
  outliers start: 13
  outliers final: 12
  residues processed: 142
  average time/residue: 1.5110
  time to fit residues: 228.0740
Evaluate side-chains
  129 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 116 optimal weight:    4.9990
   chunk 95 optimal weight:    9.9990
   chunk 73 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   overall best weight:    2.2184

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.152030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.133703 restraints weight = 7372.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 0.63
r_work: 0.3329 rms_B_bonded: 1.06 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 1.82 restraints_weight: 0.2500
r_work: 0.3063 rms_B_bonded: 4.92 restraints_weight: 0.1250
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10216  Z= 0.203
  Angle     :  0.636   7.581  13848  Z= 0.356
  Chirality :  0.050   0.255   1576
  Planarity :  0.006   0.060   1796
  Dihedral  :  4.794  18.288   1412
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.93 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1328
  helix:  1.48 (0.26), residues: 392
  sheet: -0.28 (0.39), residues: 176
  loop : -0.04 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  87 
 HIS   0.004   0.001   HIS B  53 
 PHE   0.013   0.002   PHE A 233 
 TYR   0.016   0.002   TYR A 314 
 ARG   0.002   0.000   ARG C  16 

*********************** 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
  140 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.149 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8105 (m-30) cc_final: 0.7885 (m-30)
REVERT: A  138 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7270 (pm20)
REVERT: A  331 MET cc_start: 0.8209 (mtp) cc_final: 0.7923 (mtp)
REVERT: B   29 ASP cc_start: 0.8128 (m-30) cc_final: 0.7915 (m-30)
REVERT: B  138 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7268 (pm20)
REVERT: B  331 MET cc_start: 0.8210 (mtp) cc_final: 0.7928 (mtp)
REVERT: C   29 ASP cc_start: 0.8129 (m-30) cc_final: 0.7913 (m-30)
REVERT: C  138 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7283 (pm20)
REVERT: C  331 MET cc_start: 0.8211 (mtp) cc_final: 0.7927 (mtp)
REVERT: D   29 ASP cc_start: 0.8129 (m-30) cc_final: 0.7911 (m-30)
REVERT: D  138 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7269 (pm20)
REVERT: D  331 MET cc_start: 0.8209 (mtp) cc_final: 0.7926 (mtp)
  outliers start: 22
  outliers final: 16
  residues processed: 135
  average time/residue: 1.5864
  time to fit residues: 227.4415
Evaluate side-chains
  134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 112 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   chunk 100 optimal weight:    0.8980
   chunk 108 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   overall best weight:    2.1384

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.151871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.133498 restraints weight = 7272.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 0.63
r_work: 0.3333 rms_B_bonded: 1.06 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work: 0.3069 rms_B_bonded: 4.89 restraints_weight: 0.1250
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10216  Z= 0.200
  Angle     :  0.631   7.725  13848  Z= 0.353
  Chirality :  0.049   0.242   1576
  Planarity :  0.006   0.062   1796
  Dihedral  :  4.843  18.958   1412
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1328
  helix:  1.47 (0.26), residues: 392
  sheet: -0.30 (0.39), residues: 176
  loop : -0.03 (0.25), residues: 760

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

*********************** 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
  142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 1.167 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8075 (m-30) cc_final: 0.7874 (m-30)
REVERT: A  138 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7297 (pm20)
REVERT: A  331 MET cc_start: 0.8240 (mtp) cc_final: 0.7844 (mtp)
REVERT: B  138 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7284 (pm20)
REVERT: B  331 MET cc_start: 0.8226 (mtp) cc_final: 0.7827 (mtp)
REVERT: C  138 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7310 (pm20)
REVERT: C  331 MET cc_start: 0.8234 (mtp) cc_final: 0.7837 (mtp)
REVERT: D  138 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7303 (pm20)
REVERT: D  331 MET cc_start: 0.8233 (mtp) cc_final: 0.7836 (mtp)
  outliers start: 25
  outliers final: 20
  residues processed: 138
  average time/residue: 1.5500
  time to fit residues: 227.2922
Evaluate side-chains
  139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 118 optimal weight:    8.9990
   chunk 103 optimal weight:    0.3980
   chunk 69 optimal weight:    3.9990
   chunk 125 optimal weight:    0.4980
   chunk 59 optimal weight:    0.4980
   chunk 99 optimal weight:   20.0000
   chunk 60 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.151941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.133293 restraints weight = 7257.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 0.64
r_work: 0.3337 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 1.86 restraints_weight: 0.2500
r_work: 0.3073 rms_B_bonded: 4.94 restraints_weight: 0.1250
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10216  Z= 0.186
  Angle     :  0.611   7.756  13848  Z= 0.342
  Chirality :  0.048   0.232   1576
  Planarity :  0.005   0.062   1796
  Dihedral  :  4.819  19.556   1412
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.16 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.24), residues: 1328
  helix:  1.49 (0.27), residues: 392
  sheet: -0.28 (0.39), residues: 176
  loop : -0.03 (0.25), residues: 760

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

*********************** 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
  138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.110 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7273 (pm20)
REVERT: A  331 MET cc_start: 0.8234 (mtp) cc_final: 0.7861 (mtp)
REVERT: B  138 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7267 (pm20)
REVERT: B  250 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7880 (mt-10)
REVERT: B  331 MET cc_start: 0.8208 (mtp) cc_final: 0.7839 (mtp)
REVERT: C  138 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7297 (pm20)
REVERT: C  250 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7881 (mt-10)
REVERT: C  331 MET cc_start: 0.8221 (mtp) cc_final: 0.7848 (mtp)
REVERT: D  138 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7265 (pm20)
REVERT: D  250 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7897 (mt-10)
REVERT: D  331 MET cc_start: 0.8207 (mtp) cc_final: 0.7835 (mtp)
  outliers start: 21
  outliers final: 20
  residues processed: 134
  average time/residue: 1.5723
  time to fit residues: 223.4149
Evaluate side-chains
  137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 93 optimal weight:   20.0000
   chunk 96 optimal weight:    3.9990
   chunk 131 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   chunk 44 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 118 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.151946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.133374 restraints weight = 7269.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 0.64
r_work: 0.3299 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work: 0.3031 rms_B_bonded: 4.90 restraints_weight: 0.1250
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1899

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= 0.248
  Angle     :  0.704   9.210  13848  Z= 0.395
  Chirality :  0.052   0.293   1576
  Planarity :  0.007   0.066   1796
  Dihedral  :  5.061  18.822   1412
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.07 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.24), residues: 1328
  helix:  1.29 (0.26), residues: 392
  sheet: -0.42 (0.39), residues: 176
  loop : -0.04 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 313 
 HIS   0.005   0.001   HIS D  53 
 PHE   0.016   0.002   PHE A 233 
 TYR   0.017   0.002   TYR C 314 
 ARG   0.002   0.001   ARG B  16 

*********************** 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
  140 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 1.090 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7306 (pm20)
REVERT: A  260 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8385 (ttpp)
REVERT: A  331 MET cc_start: 0.8291 (mtp) cc_final: 0.7942 (mtp)
REVERT: B  138 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7298 (pm20)
REVERT: B  260 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8374 (ttpp)
REVERT: B  331 MET cc_start: 0.8287 (mtp) cc_final: 0.7936 (mtp)
REVERT: C  138 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7322 (pm20)
REVERT: C  260 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8385 (ttpp)
REVERT: C  331 MET cc_start: 0.8281 (mtp) cc_final: 0.7926 (mtp)
REVERT: D  138 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7287 (pm20)
REVERT: D  260 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8381 (ttpp)
REVERT: D  331 MET cc_start: 0.8290 (mtp) cc_final: 0.7939 (mtp)
  outliers start: 18
  outliers final: 16
  residues processed: 136
  average time/residue: 1.5944
  time to fit residues: 229.4923
Evaluate side-chains
  134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 87 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 93 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.151826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.133154 restraints weight = 7378.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 0.64
r_work: 0.3326 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 1.87 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10216  Z= 0.191
  Angle     :  0.622   8.494  13848  Z= 0.348
  Chirality :  0.049   0.239   1576
  Planarity :  0.006   0.066   1796
  Dihedral  :  4.911  19.408   1412
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.26 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1328
  helix:  1.45 (0.26), residues: 392
  sheet: -0.25 (0.39), residues: 176
  loop : -0.04 (0.25), residues: 760

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

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

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 1.232 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7216 (pm20)
REVERT: A  260 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8149 (ttpp)
REVERT: A  331 MET cc_start: 0.8222 (mtp) cc_final: 0.7868 (mtp)
REVERT: B  138 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7220 (pm20)
REVERT: B  260 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8140 (ttpp)
REVERT: B  331 MET cc_start: 0.8221 (mtp) cc_final: 0.7870 (mtp)
REVERT: C  138 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7227 (pm20)
REVERT: C  260 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8136 (ttpp)
REVERT: C  331 MET cc_start: 0.8219 (mtp) cc_final: 0.7866 (mtp)
REVERT: D  138 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7216 (pm20)
REVERT: D  260 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8147 (ttpp)
REVERT: D  331 MET cc_start: 0.8219 (mtp) cc_final: 0.7869 (mtp)
  outliers start: 24
  outliers final: 20
  residues processed: 140
  average time/residue: 1.6161
  time to fit residues: 239.6868
Evaluate side-chains
  139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 125 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 70 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   overall best weight:    3.1786

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.150060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.131313 restraints weight = 7285.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 0.63
r_work: 0.3298 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 1.86 restraints_weight: 0.2500
r_work: 0.3031 rms_B_bonded: 4.95 restraints_weight: 0.1250
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1930

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= 0.248
  Angle     :  0.712   9.884  13848  Z= 0.399
  Chirality :  0.052   0.284   1576
  Planarity :  0.007   0.067   1796
  Dihedral  :  5.095  18.705   1412
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.35 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.24), residues: 1328
  helix:  1.27 (0.26), residues: 392
  sheet: -0.38 (0.39), residues: 176
  loop : -0.08 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 313 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.016   0.002   PHE D 233 
 TYR   0.017   0.002   TYR A 314 
 ARG   0.003   0.001   ARG C  16 

*********************** 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
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7342 (pm20)
REVERT: A  260 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8410 (ttpp)
REVERT: A  331 MET cc_start: 0.8329 (mtp) cc_final: 0.8010 (mtp)
REVERT: B  138 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7346 (pm20)
REVERT: B  260 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8401 (ttpp)
REVERT: B  331 MET cc_start: 0.8322 (mtp) cc_final: 0.8000 (mtp)
REVERT: C  138 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7361 (pm20)
REVERT: C  260 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8410 (ttpp)
REVERT: C  331 MET cc_start: 0.8319 (mtp) cc_final: 0.7997 (mtp)
REVERT: D  138 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7331 (pm20)
REVERT: D  260 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8405 (ttpp)
REVERT: D  331 MET cc_start: 0.8329 (mtp) cc_final: 0.8008 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 137
  average time/residue: 1.6848
  time to fit residues: 244.2013
Evaluate side-chains
  135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 90 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0030
   chunk 60 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    3.5998

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.149675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.130931 restraints weight = 7240.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 0.63
r_work: 0.3298 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 1.84 restraints_weight: 0.2500
r_work: 0.3036 rms_B_bonded: 4.91 restraints_weight: 0.1250
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1968

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= 0.268
  Angle     :  0.734  10.401  13848  Z= 0.411
  Chirality :  0.053   0.276   1576
  Planarity :  0.007   0.069   1796
  Dihedral  :  5.154  18.488   1412
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.54 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.24), residues: 1328
  helix:  1.22 (0.26), residues: 392
  sheet: -0.42 (0.39), residues: 176
  loop : -0.08 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 313 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.016   0.002   PHE B 233 
 TYR   0.018   0.002   TYR B 314 
 ARG   0.003   0.001   ARG C 323 

*********************** 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
  139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.119 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7349 (pm20)
REVERT: A  260 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8399 (ttpp)
REVERT: B  138 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7345 (pm20)
REVERT: B  260 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8393 (ttpp)
REVERT: C  138 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7358 (pm20)
REVERT: C  260 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8406 (ttpp)
REVERT: D  138 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7339 (pm20)
REVERT: D  223 GLU cc_start: 0.7873 (mp0) cc_final: 0.7651 (mp0)
REVERT: D  260 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8397 (ttpp)
  outliers start: 20
  outliers final: 20
  residues processed: 135
  average time/residue: 1.6120
  time to fit residues: 230.4129
Evaluate side-chains
  139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 122 optimal weight:    0.6980
   chunk 33 optimal weight:   20.0000
   chunk 78 optimal weight:    0.3980
   chunk 69 optimal weight:    6.9990
   chunk 119 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.154118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.135841 restraints weight = 7378.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 0.64
r_work: 0.3350 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 1.86 restraints_weight: 0.2500
r_work: 0.3087 rms_B_bonded: 4.99 restraints_weight: 0.1250
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.1882

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= 0.166
  Angle     :  0.591   8.164  13848  Z= 0.330
  Chirality :  0.047   0.215   1576
  Planarity :  0.005   0.068   1796
  Dihedral  :  4.842  19.526   1412
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.54 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.24), residues: 1328
  helix:  1.55 (0.27), residues: 392
  sheet: -0.21 (0.39), residues: 176
  loop : -0.05 (0.25), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 313 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.014   0.001   PHE A 233 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.001   0.000   ARG A  16 

********************** 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
  133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7318 (pm20)
REVERT: A  223 GLU cc_start: 0.7715 (mp0) cc_final: 0.7442 (mp0)
REVERT: A  260 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8386 (ttpp)
REVERT: B  138 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7331 (pm20)
REVERT: B  223 GLU cc_start: 0.7717 (mp0) cc_final: 0.7444 (mp0)
REVERT: B  260 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8387 (ttpp)
REVERT: C  138 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7329 (pm20)
REVERT: C  223 GLU cc_start: 0.7721 (mp0) cc_final: 0.7437 (mp0)
REVERT: C  260 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8388 (ttpp)
REVERT: D  138 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7300 (pm20)
REVERT: D  260 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8385 (ttpp)
  outliers start: 20
  outliers final: 20
  residues processed: 129
  average time/residue: 1.6776
  time to fit residues: 228.6529
Evaluate side-chains
  133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  271 LYS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  271 LYS
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  271 LYS
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 25 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 124 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 118 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 93 optimal weight:   20.0000
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.151804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.133242 restraints weight = 7262.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 0.63
r_work: 0.3311 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work: 0.3045 rms_B_bonded: 4.91 restraints_weight: 0.1250
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10216  Z= 0.216
  Angle     :  0.670   9.532  13848  Z= 0.375
  Chirality :  0.050   0.255   1576
  Planarity :  0.006   0.067   1796
  Dihedral  :  5.011  19.465   1412
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.92 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.24), residues: 1328
  helix:  1.41 (0.26), residues: 392
  sheet: -0.23 (0.39), residues: 176
  loop : -0.11 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  87 
 HIS   0.004   0.001   HIS C  53 
 PHE   0.015   0.002   PHE D 233 
 TYR   0.016   0.002   TYR B 314 
 ARG   0.002   0.000   ARG A  16 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10234.97 seconds
wall clock time: 180 minutes 42.91 seconds (10842.91 seconds total)