Starting phenix.real_space_refine
on Wed Jul 30 22:29:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d66_27218/07_2025/8d66_27218_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d66_27218/07_2025/8d66_27218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d66_27218/07_2025/8d66_27218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d66_27218/07_2025/8d66_27218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d66_27218/07_2025/8d66_27218_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d66_27218/07_2025/8d66_27218_neut.cif"
  }
  resolution = 3.14
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S      35      5.16       5
     C    8375      2.51       5
     N    2085      2.21       5
     O    2300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12800
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "A"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 55
          Unusual residues: {'DHL': 1, 'PGW': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.51, per 1000 atoms: 0.43
  Number of scatterers: 12800
  At special positions: 0
  Unit cell: (90.2, 90.2, 125.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P       5     15.00
     O    2300      8.00
     N    2085      7.00
     C    8375      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: 2.95
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 10 sheets defined
      34.1% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.542A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN A  69 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 153
      removed outlier: 3.542A  pdb=" N   ILE A 152 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP A 153 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 149 through 153'
    Processing helix  chain 'A' and resid 201 through 209
      removed outlier: 3.860A  pdb=" N   ILE A 209 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 221
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 227 through 249
    Processing helix  chain 'A' and resid 260 through 285
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.682A  pdb=" N   LEU A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.541A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN B  69 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 153
      removed outlier: 3.543A  pdb=" N   ILE B 152 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP B 153 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 149 through 153'
    Processing helix  chain 'B' and resid 201 through 209
      removed outlier: 3.860A  pdb=" N   ILE B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 221
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 227 through 249
    Processing helix  chain 'B' and resid 260 through 285
    Processing helix  chain 'B' and resid 302 through 317
      removed outlier: 3.681A  pdb=" N   LEU B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.541A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN C  69 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 153
      removed outlier: 3.542A  pdb=" N   ILE C 152 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP C 153 " --> pdb=" O   GLU C 150 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 149 through 153'
    Processing helix  chain 'C' and resid 201 through 209
      removed outlier: 3.861A  pdb=" N   ILE C 209 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 221
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 227 through 249
    Processing helix  chain 'C' and resid 260 through 285
    Processing helix  chain 'C' and resid 302 through 317
      removed outlier: 3.681A  pdb=" N   LEU C 306 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE C 308 " --> pdb=" O   PHE C 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.541A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN D  69 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 153
      removed outlier: 3.542A  pdb=" N   ILE D 152 " --> pdb=" O   THR D 149 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP D 153 " --> pdb=" O   GLU D 150 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 149 through 153'
    Processing helix  chain 'D' and resid 201 through 209
      removed outlier: 3.861A  pdb=" N   ILE D 209 " --> pdb=" O   LEU D 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 221
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 227 through 249
    Processing helix  chain 'D' and resid 260 through 285
    Processing helix  chain 'D' and resid 302 through 317
      removed outlier: 3.682A  pdb=" N   LEU D 306 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE D 308 " --> pdb=" O   PHE D 304 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.541A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN E  69 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 153
      removed outlier: 3.542A  pdb=" N   ILE E 152 " --> pdb=" O   THR E 149 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP E 153 " --> pdb=" O   GLU E 150 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 149 through 153'
    Processing helix  chain 'E' and resid 201 through 209
      removed outlier: 3.860A  pdb=" N   ILE E 209 " --> pdb=" O   LEU E 205 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 221
    Processing helix  chain 'E' and resid 222 through 225
    Processing helix  chain 'E' and resid 227 through 249
    Processing helix  chain 'E' and resid 260 through 285
    Processing helix  chain 'E' and resid 302 through 317
      removed outlier: 3.681A  pdb=" N   LEU E 306 " --> pdb=" O   LEU E 302 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE E 308 " --> pdb=" O   PHE E 304 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.238A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN A  42 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.712A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ASP A 196 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   LYS A 165 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   VAL A 198 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ARG A 163 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 58
      removed outlier: 6.237A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN B  42 " --> pdb=" O   SER B  15 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.712A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ASP B 196 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   VAL B 198 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ARG B 163 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58
      removed outlier: 6.237A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN C  42 " --> pdb=" O   SER C  15 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.712A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   ASP C 196 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LYS C 165 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   VAL C 198 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ARG C 163 " --> pdb=" O   VAL C 198 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 58
      removed outlier: 6.237A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN D  42 " --> pdb=" O   SER D  15 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.712A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   ASP D 196 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   LYS D 165 " --> pdb=" O   ASP D 196 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   VAL D 198 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ARG D 163 " --> pdb=" O   VAL D 198 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 58
      removed outlier: 6.237A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN E  42 " --> pdb=" O   SER E  15 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.712A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ASP E 196 " --> pdb=" O   LYS E 165 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LYS E 165 " --> pdb=" O   ASP E 196 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   VAL E 198 " --> pdb=" O   ARG E 163 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ARG E 163 " --> pdb=" O   VAL E 198 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1650 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: 3.89

  Time building geometry restraints manager: 3.53 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2021
        1.31 -     1.43: 3759
        1.43 -     1.56: 7285
        1.56 -     1.68: 10
        1.68 -     1.81: 55
  Bond restraints: 13130
  Sorted by residual:
  bond pdb=" C1  PGW C 401 "
       pdb=" O01 PGW C 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.402 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C1  PGW A 401 "
       pdb=" O01 PGW A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.402 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C1  PGW D 401 "
       pdb=" O01 PGW D 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.402 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C1  PGW E 401 "
       pdb=" O01 PGW E 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.401 -0.069 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C19 PGW A 401 "
       pdb=" O03 PGW A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.401 -0.069 2.00e-02 2.50e+03 1.20e+01
  ... (remaining 13125 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 17160
        2.34 -     4.69: 550
        4.69 -     7.03: 95
        7.03 -     9.38: 5
        9.38 -    11.72: 15
  Bond angle restraints: 17825
  Sorted by residual:
  angle pdb=" O11 PGW C 401 "
        pdb=" P   PGW C 401 "
        pdb=" O12 PGW C 401 "
      ideal   model   delta    sigma   weight residual
      98.90  110.62  -11.72 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" O11 PGW A 401 "
        pdb=" P   PGW A 401 "
        pdb=" O12 PGW A 401 "
      ideal   model   delta    sigma   weight residual
      98.90  110.59  -11.69 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" O11 PGW B 401 "
        pdb=" P   PGW B 401 "
        pdb=" O12 PGW B 401 "
      ideal   model   delta    sigma   weight residual
      98.90  110.58  -11.68 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" O11 PGW E 401 "
        pdb=" P   PGW E 401 "
        pdb=" O12 PGW E 401 "
      ideal   model   delta    sigma   weight residual
      98.90  110.58  -11.68 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" O11 PGW D 401 "
        pdb=" P   PGW D 401 "
        pdb=" O12 PGW D 401 "
      ideal   model   delta    sigma   weight residual
      98.90  110.56  -11.66 3.00e+00 1.11e-01 1.51e+01
  ... (remaining 17820 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.71: 7531
       34.71 -    69.42: 184
       69.42 -   104.12: 20
      104.12 -   138.83: 25
      138.83 -   173.54: 5
  Dihedral angle restraints: 7765
    sinusoidal: 3260
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  LEU B 118 "
           pdb=" C   LEU B 118 "
           pdb=" N   PHE B 119 "
           pdb=" CA  PHE B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.11  -25.89     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  LEU E 118 "
           pdb=" C   LEU E 118 "
           pdb=" N   PHE E 119 "
           pdb=" CA  PHE E 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.12  -25.88     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  LEU C 118 "
           pdb=" C   LEU C 118 "
           pdb=" N   PHE C 119 "
           pdb=" CA  PHE C 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.14  -25.86     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 7762 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1385
       0.057 -    0.115: 438
       0.115 -    0.172: 107
       0.172 -    0.230: 25
       0.230 -    0.287: 5
  Chirality restraints: 1960
  Sorted by residual:
  chirality pdb=" CA  THR C  61 "
            pdb=" N   THR C  61 "
            pdb=" C   THR C  61 "
            pdb=" CB  THR C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CA  THR B  61 "
            pdb=" N   THR B  61 "
            pdb=" C   THR B  61 "
            pdb=" CB  THR B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  THR E  61 "
            pdb=" N   THR E  61 "
            pdb=" C   THR E  61 "
            pdb=" CB  THR E  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 1957 not shown)

  Planarity restraints: 2250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 206 "    0.021 2.00e-02 2.50e+03   1.65e-02 6.80e+00
        pdb=" CG  TRP D 206 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 206 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 206 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 206 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 206 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 206 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 206 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 206 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 206 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 206 "   -0.021 2.00e-02 2.50e+03   1.65e-02 6.78e+00
        pdb=" CG  TRP A 206 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 206 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 206 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 206 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 206 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 206 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 206 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 206 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 206 "   -0.021 2.00e-02 2.50e+03   1.64e-02 6.70e+00
        pdb=" CG  TRP E 206 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 206 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 206 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 206 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 206 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 206 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 206 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 206 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 206 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2247 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3871
        2.83 -     3.35: 10813
        3.35 -     3.86: 20302
        3.86 -     4.38: 24375
        4.38 -     4.90: 42848
  Nonbonded interactions: 102209
  Sorted by model distance:
  nonbonded pdb=" O   SER D 221 "
            pdb=" OG  SER D 221 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   SER C 221 "
            pdb=" OG  SER C 221 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   SER E 221 "
            pdb=" OG  SER E 221 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   SER A 221 "
            pdb=" OG  SER A 221 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   SER B 221 "
            pdb=" OG  SER B 221 "
     model   vdw
     2.309 3.040
  ... (remaining 102204 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  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:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     28.470
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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      :  0.009   0.070  13130  Z= 0.379
  Angle     :  1.018  11.720  17825  Z= 0.512
  Chirality :  0.061   0.287   1960
  Planarity :  0.005   0.039   2250
  Dihedral  : 18.545 173.540   4855
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.21), residues: 1525
  helix: -0.19 (0.22), residues: 515
  sheet:  0.28 (0.28), residues: 395
  loop : -2.85 (0.21), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP C 206 
 HIS   0.004   0.002   HIS A 177 
 PHE   0.016   0.002   PHE D 228 
 TYR   0.023   0.003   TYR D 245 
 ARG   0.007   0.001   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11013 (  560)
  hydrogen bonds       : angle       6.10448 ( 1650)
  covalent geometry    : bond        0.00903 (13130)
  covalent geometry    : angle       1.01830 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8835 (mttt) cc_final: 0.8462 (mtmt)
REVERT: A   86 ASP cc_start: 0.7856 (t0) cc_final: 0.7374 (t70)
REVERT: A  174 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7352 (ttt-90)
REVERT: B   54 LYS cc_start: 0.8558 (mttt) cc_final: 0.8270 (mtmt)
REVERT: B   65 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.7151 (mtm180)
REVERT: B   86 ASP cc_start: 0.7812 (t0) cc_final: 0.7449 (t70)
REVERT: B   90 LYS cc_start: 0.8884 (pttt) cc_final: 0.8651 (ptpp)
REVERT: C  114 MET cc_start: 0.9024 (mtt) cc_final: 0.8761 (mtt)
REVERT: C  265 MET cc_start: 0.8348 (mtp) cc_final: 0.8076 (mtp)
REVERT: D   86 ASP cc_start: 0.7720 (t0) cc_final: 0.7269 (t70)
REVERT: D  113 ASP cc_start: 0.7273 (m-30) cc_final: 0.7059 (p0)
REVERT: E   21 ASN cc_start: 0.8540 (t0) cc_final: 0.8186 (t0)
REVERT: E   54 LYS cc_start: 0.8752 (mttt) cc_final: 0.8133 (mtpp)
REVERT: E   86 ASP cc_start: 0.7912 (t0) cc_final: 0.7397 (t70)
REVERT: E  113 ASP cc_start: 0.7200 (m-30) cc_final: 0.6796 (p0)
REVERT: E  174 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7351 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2873
  time to fit residues: 63.7225
Evaluate side-chains
  136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 136 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
B  27 ASN
C  27 ASN
D  27 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.157542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.118092 restraints weight = 13110.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.53
r_work: 0.3019 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13130  Z= 0.132
  Angle     :  0.559   5.277  17825  Z= 0.285
  Chirality :  0.047   0.174   1960
  Planarity :  0.004   0.036   2250
  Dihedral  : 14.726  91.858   1925
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  4.95 %
    Favored  : 93.89 %
  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: -0.76 (0.22), residues: 1525
  helix:  0.97 (0.24), residues: 515
  sheet:  0.54 (0.28), residues: 395
  loop : -2.61 (0.22), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 206 
 HIS   0.002   0.001   HIS A 177 
 PHE   0.011   0.001   PHE D 236 
 TYR   0.015   0.001   TYR C 245 
 ARG   0.002   0.000   ARG C 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  560)
  hydrogen bonds       : angle       4.56290 ( 1650)
  covalent geometry    : bond        0.00299 (13130)
  covalent geometry    : angle       0.55858 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.367 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.8999 (mttt) cc_final: 0.8628 (mtmt)
REVERT: A   86 ASP cc_start: 0.8147 (t0) cc_final: 0.7536 (t70)
REVERT: A  174 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7969 (ttt-90)
REVERT: A  223 PHE cc_start: 0.8312 (m-80) cc_final: 0.7718 (m-80)
REVERT: A  245 TYR cc_start: 0.7653 (m-80) cc_final: 0.7010 (m-80)
REVERT: B   54 LYS cc_start: 0.8675 (mttt) cc_final: 0.8456 (mtmt)
REVERT: B   65 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7464 (mtm180)
REVERT: B   86 ASP cc_start: 0.8130 (t0) cc_final: 0.7684 (t70)
REVERT: B   90 LYS cc_start: 0.8961 (pttt) cc_final: 0.8748 (ptpp)
REVERT: C  265 MET cc_start: 0.8132 (mtp) cc_final: 0.7735 (mtp)
REVERT: D   86 ASP cc_start: 0.7959 (t0) cc_final: 0.7343 (t70)
REVERT: D  113 ASP cc_start: 0.7954 (m-30) cc_final: 0.7254 (p0)
REVERT: D  174 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7929 (ttt-90)
REVERT: E   86 ASP cc_start: 0.8175 (t0) cc_final: 0.7578 (t70)
REVERT: E  113 ASP cc_start: 0.7814 (m-30) cc_final: 0.7161 (p0)
REVERT: E  114 MET cc_start: 0.9139 (mtt) cc_final: 0.8735 (mtt)
REVERT: E  174 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8123 (ttm-80)
  outliers start: 16
  outliers final: 11
  residues processed: 148
  average time/residue: 0.2803
  time to fit residues: 58.5533
Evaluate side-chains
  130 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  259 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 126 optimal weight:    0.4980
   chunk 134 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0980
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 127 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
D 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.156045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.116222 restraints weight = 13193.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.64
r_work: 0.3173 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13130  Z= 0.152
  Angle     :  0.547   6.166  17825  Z= 0.281
  Chirality :  0.048   0.199   1960
  Planarity :  0.004   0.030   2250
  Dihedral  : 12.788  89.996   1925
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  6.76 %
    Favored  : 91.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.23), residues: 1525
  helix:  1.28 (0.24), residues: 525
  sheet:  0.66 (0.28), residues: 395
  loop : -2.34 (0.23), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 206 
 HIS   0.003   0.001   HIS D 177 
 PHE   0.011   0.001   PHE E 236 
 TYR   0.016   0.001   TYR D 245 
 ARG   0.005   0.000   ARG E  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  560)
  hydrogen bonds       : angle       4.36065 ( 1650)
  covalent geometry    : bond        0.00367 (13130)
  covalent geometry    : angle       0.54701 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 1.347 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.9133 (mttt) cc_final: 0.8837 (mtmt)
REVERT: A   86 ASP cc_start: 0.8363 (t0) cc_final: 0.7756 (t70)
REVERT: A  174 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7940 (mtp85)
REVERT: B   65 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.7846 (mtm180)
REVERT: B   86 ASP cc_start: 0.8226 (t0) cc_final: 0.7741 (t70)
REVERT: C  245 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7519 (t80)
REVERT: D   65 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8087 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8212 (t0) cc_final: 0.7746 (t70)
REVERT: D  174 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.8026 (ttt-90)
REVERT: D  245 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7499 (t80)
REVERT: E   65 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7819 (mtm180)
REVERT: E  113 ASP cc_start: 0.8152 (m-30) cc_final: 0.7661 (p0)
REVERT: E  174 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8105 (ttm-80)
REVERT: E  245 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.6765 (t80)
  outliers start: 29
  outliers final: 21
  residues processed: 148
  average time/residue: 0.3061
  time to fit residues: 62.8551
Evaluate side-chains
  144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 91 optimal weight:    0.0970
   chunk 22 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 135 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 142 optimal weight:    3.9990
   chunk 145 optimal weight:    5.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
D 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.157543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.117396 restraints weight = 13078.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.53
r_work: 0.3021 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13130  Z= 0.121
  Angle     :  0.509   5.233  17825  Z= 0.260
  Chirality :  0.047   0.207   1960
  Planarity :  0.003   0.032   2250
  Dihedral  : 11.725  82.700   1925
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  7.56 %
    Favored  : 89.89 %
  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: -0.16 (0.23), residues: 1525
  helix:  1.47 (0.24), residues: 525
  sheet:  0.79 (0.28), residues: 395
  loop : -2.27 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 206 
 HIS   0.002   0.001   HIS E 177 
 PHE   0.017   0.001   PHE B 236 
 TYR   0.014   0.001   TYR D 245 
 ARG   0.004   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03378 (  560)
  hydrogen bonds       : angle       4.16393 ( 1650)
  covalent geometry    : bond        0.00283 (13130)
  covalent geometry    : angle       0.50876 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 1.551 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.8886 (mttt) cc_final: 0.8579 (mtmt)
REVERT: A   86 ASP cc_start: 0.8228 (t0) cc_final: 0.7583 (t70)
REVERT: A  174 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7823 (mtp85)
REVERT: A  187 GLU cc_start: 0.7860 (tt0) cc_final: 0.7582 (tt0)
REVERT: B   65 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7491 (mtm180)
REVERT: B   86 ASP cc_start: 0.8114 (t0) cc_final: 0.7644 (t70)
REVERT: C   34 LYS cc_start: 0.9143 (mttt) cc_final: 0.8900 (mttp)
REVERT: C   86 ASP cc_start: 0.8169 (t0) cc_final: 0.7790 (t70)
REVERT: C  245 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7134 (t80)
REVERT: D   65 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7650 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8098 (t0) cc_final: 0.7640 (t70)
REVERT: D  174 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7775 (ttt-90)
REVERT: D  245 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: E   65 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7434 (mtm180)
REVERT: E  113 ASP cc_start: 0.7888 (m-30) cc_final: 0.7275 (p0)
REVERT: E  245 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6306 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 156
  average time/residue: 0.3229
  time to fit residues: 71.8774
Evaluate side-chains
  151 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 1.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0050
   chunk 6 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0970
   chunk 19 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 116 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.4198

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
D 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.156653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.112972 restraints weight = 13169.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.64
r_work: 0.3101 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13130  Z= 0.131
  Angle     :  0.515   5.063  17825  Z= 0.264
  Chirality :  0.048   0.207   1960
  Planarity :  0.003   0.035   2250
  Dihedral  : 11.155  80.499   1925
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  :  8.44 %
    Favored  : 88.80 %
  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: -0.04 (0.23), residues: 1525
  helix:  1.64 (0.23), residues: 525
  sheet:  0.81 (0.28), residues: 395
  loop : -2.24 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 206 
 HIS   0.002   0.001   HIS E 177 
 PHE   0.016   0.001   PHE C 236 
 TYR   0.015   0.001   TYR D 245 
 ARG   0.004   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  560)
  hydrogen bonds       : angle       4.12055 ( 1650)
  covalent geometry    : bond        0.00311 (13130)
  covalent geometry    : angle       0.51494 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 1.388 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.8938 (mttt) cc_final: 0.8689 (mtmt)
REVERT: A   86 ASP cc_start: 0.8130 (t0) cc_final: 0.7556 (t70)
REVERT: A  137 ASN cc_start: 0.8770 (p0) cc_final: 0.8508 (p0)
REVERT: A  174 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7794 (mtp85)
REVERT: B   65 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7666 (mtm180)
REVERT: B   86 ASP cc_start: 0.8007 (t0) cc_final: 0.7589 (t70)
REVERT: C  174 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7810 (ttm-80)
REVERT: C  245 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7481 (t80)
REVERT: D   65 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7875 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8120 (t0) cc_final: 0.7687 (t70)
REVERT: D  174 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7819 (ttt-90)
REVERT: D  245 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7461 (t80)
REVERT: E   65 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7662 (mtm180)
REVERT: E  113 ASP cc_start: 0.7869 (m-30) cc_final: 0.7522 (p0)
REVERT: E  174 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7878 (mtp85)
REVERT: E  245 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6659 (t80)
  outliers start: 38
  outliers final: 31
  residues processed: 155
  average time/residue: 0.3087
  time to fit residues: 68.0173
Evaluate side-chains
  152 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 1.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 145 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 130 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 70 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.170699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.131403 restraints weight = 13316.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.52
r_work: 0.2949 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13130  Z= 0.209
  Angle     :  0.583   5.562  17825  Z= 0.299
  Chirality :  0.050   0.211   1960
  Planarity :  0.004   0.038   2250
  Dihedral  : 11.241  88.113   1925
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  :  8.87 %
    Favored  : 88.15 %
  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: -0.11 (0.23), residues: 1525
  helix:  1.62 (0.23), residues: 530
  sheet:  0.63 (0.28), residues: 395
  loop : -2.24 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 206 
 HIS   0.003   0.001   HIS E 177 
 PHE   0.014   0.002   PHE D 236 
 TYR   0.019   0.002   TYR D 245 
 ARG   0.006   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  560)
  hydrogen bonds       : angle       4.32510 ( 1650)
  covalent geometry    : bond        0.00519 (13130)
  covalent geometry    : angle       0.58253 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 2.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8983 (mttt) cc_final: 0.8645 (mtmt)
REVERT: B   65 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7534 (mtm180)
REVERT: B   86 ASP cc_start: 0.8175 (t0) cc_final: 0.7680 (t70)
REVERT: C  245 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.7066 (t80)
REVERT: D   65 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7764 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8112 (t0) cc_final: 0.7638 (t70)
REVERT: D  245 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7083 (t80)
REVERT: D  263 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7928 (m-30)
REVERT: E   65 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7453 (mtm180)
REVERT: E  113 ASP cc_start: 0.7847 (m-30) cc_final: 0.7311 (p0)
REVERT: E  174 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7895 (ttm-80)
REVERT: E  245 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.6316 (t80)
REVERT: E  263 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8111 (m-30)
  outliers start: 41
  outliers final: 30
  residues processed: 148
  average time/residue: 0.3473
  time to fit residues: 72.2164
Evaluate side-chains
  151 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 116
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 127 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 144 optimal weight:    7.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 124 GLN
A 182 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.155282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.114563 restraints weight = 13174.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.49
r_work: 0.2997 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13130  Z= 0.134
  Angle     :  0.523   5.111  17825  Z= 0.268
  Chirality :  0.048   0.217   1960
  Planarity :  0.003   0.035   2250
  Dihedral  : 10.666  82.124   1925
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  :  9.53 %
    Favored  : 87.35 %
  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: -0.02 (0.23), residues: 1525
  helix:  1.76 (0.23), residues: 525
  sheet:  1.07 (0.30), residues: 345
  loop : -2.26 (0.23), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 206 
 HIS   0.002   0.001   HIS E 177 
 PHE   0.014   0.001   PHE D 236 
 TYR   0.016   0.001   TYR D 245 
 ARG   0.007   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  560)
  hydrogen bonds       : angle       4.14834 ( 1650)
  covalent geometry    : bond        0.00318 (13130)
  covalent geometry    : angle       0.52265 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 125
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8905 (mttt) cc_final: 0.8590 (mtmt)
REVERT: B   65 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7499 (mtm180)
REVERT: B   86 ASP cc_start: 0.8098 (t0) cc_final: 0.7628 (t70)
REVERT: C  174 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7688 (ttm-80)
REVERT: C  245 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.7105 (t80)
REVERT: D   65 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7718 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8063 (t0) cc_final: 0.7563 (t70)
REVERT: D  162 ILE cc_start: 0.8482 (mm) cc_final: 0.8151 (mm)
REVERT: D  187 GLU cc_start: 0.7887 (tt0) cc_final: 0.7611 (tt0)
REVERT: D  245 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.7131 (t80)
REVERT: D  263 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7692 (m-30)
REVERT: E   65 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7414 (mtm180)
REVERT: E  113 ASP cc_start: 0.7761 (m-30) cc_final: 0.7256 (p0)
REVERT: E  174 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7772 (mtp85)
REVERT: E  245 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6288 (t80)
REVERT: E  263 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7850 (m-30)
  outliers start: 43
  outliers final: 31
  residues processed: 152
  average time/residue: 0.2708
  time to fit residues: 58.8708
Evaluate side-chains
  156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 125 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 146 optimal weight:    8.9990
   chunk 118 optimal weight:    0.9990
   chunk 88 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.155301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.114439 restraints weight = 13273.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.50
r_work: 0.2997 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13130  Z= 0.136
  Angle     :  0.523   5.182  17825  Z= 0.268
  Chirality :  0.048   0.217   1960
  Planarity :  0.003   0.036   2250
  Dihedral  : 10.389  79.528   1925
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  9.38 %
    Favored  : 87.35 %
  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: -0.02 (0.23), residues: 1525
  helix:  1.81 (0.23), residues: 525
  sheet:  1.06 (0.30), residues: 345
  loop : -2.30 (0.23), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 206 
 HIS   0.002   0.001   HIS E 177 
 PHE   0.013   0.001   PHE D 236 
 TYR   0.016   0.001   TYR D 245 
 ARG   0.007   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  560)
  hydrogen bonds       : angle       4.11722 ( 1650)
  covalent geometry    : bond        0.00325 (13130)
  covalent geometry    : angle       0.52331 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 131
  time to evaluate  : 1.331 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8922 (mttt) cc_final: 0.8610 (mtmt)
REVERT: A   86 ASP cc_start: 0.8232 (t0) cc_final: 0.7555 (t70)
REVERT: A  114 MET cc_start: 0.9272 (mtt) cc_final: 0.8957 (mtt)
REVERT: B   65 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7542 (mtm180)
REVERT: B   86 ASP cc_start: 0.8167 (t0) cc_final: 0.7689 (t70)
REVERT: C   86 ASP cc_start: 0.8203 (t0) cc_final: 0.7801 (t70)
REVERT: C  174 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7723 (ttm-80)
REVERT: C  245 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.7234 (t80)
REVERT: D   65 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7757 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8097 (t0) cc_final: 0.7596 (t70)
REVERT: D  162 ILE cc_start: 0.8489 (mm) cc_final: 0.8140 (mm)
REVERT: D  245 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.7193 (t80)
REVERT: D  263 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7561 (m-30)
REVERT: E   65 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.7443 (mtm180)
REVERT: E  113 ASP cc_start: 0.7713 (m-30) cc_final: 0.7269 (p0)
REVERT: E  245 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6327 (t80)
REVERT: E  263 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7885 (m-30)
REVERT: E  265 MET cc_start: 0.8130 (mtp) cc_final: 0.7815 (mtp)
  outliers start: 45
  outliers final: 36
  residues processed: 159
  average time/residue: 0.2748
  time to fit residues: 63.1574
Evaluate side-chains
  167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 126
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 118 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
D 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.155085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.114394 restraints weight = 13186.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.57
r_work: 0.2977 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13130  Z= 0.149
  Angle     :  0.533   5.256  17825  Z= 0.273
  Chirality :  0.049   0.219   1960
  Planarity :  0.003   0.036   2250
  Dihedral  : 10.278  78.988   1925
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  :  9.53 %
    Favored  : 87.27 %
  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:  0.00 (0.23), residues: 1525
  helix:  1.85 (0.23), residues: 525
  sheet:  1.07 (0.30), residues: 345
  loop : -2.30 (0.23), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 206 
 HIS   0.003   0.001   HIS E 177 
 PHE   0.014   0.001   PHE D 236 
 TYR   0.017   0.001   TYR D 245 
 ARG   0.008   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03510 (  560)
  hydrogen bonds       : angle       4.13493 ( 1650)
  covalent geometry    : bond        0.00360 (13130)
  covalent geometry    : angle       0.53263 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 123
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8951 (mttt) cc_final: 0.8655 (mtmt)
REVERT: B   54 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8425 (mtmt)
REVERT: B   65 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7631 (mtm180)
REVERT: B   86 ASP cc_start: 0.8185 (t0) cc_final: 0.7703 (t70)
REVERT: C  174 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7769 (ttm-80)
REVERT: C  245 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7381 (t80)
REVERT: D   65 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7837 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8131 (t0) cc_final: 0.7618 (t70)
REVERT: D  162 ILE cc_start: 0.8600 (mm) cc_final: 0.8253 (mm)
REVERT: D  245 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.7324 (t80)
REVERT: D  263 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7617 (m-30)
REVERT: E   65 ARG cc_start: 0.7815 (mtp-110) cc_final: 0.7459 (mtm180)
REVERT: E  113 ASP cc_start: 0.7704 (m-30) cc_final: 0.7465 (p0)
REVERT: E  174 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7933 (mtp85)
REVERT: E  245 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6452 (t80)
REVERT: E  263 ASP cc_start: 0.8260 (t0) cc_final: 0.7914 (m-30)
  outliers start: 44
  outliers final: 38
  residues processed: 152
  average time/residue: 0.2698
  time to fit residues: 58.7287
Evaluate side-chains
  164 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 122
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  227 SER
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  259 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 132 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 133 optimal weight:    0.7980
   chunk 125 optimal weight:    0.7980
   chunk 144 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 177 HIS
A 182 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.157981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.116456 restraints weight = 13110.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.48
r_work: 0.3032 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13130  Z= 0.103
  Angle     :  0.491   5.431  17825  Z= 0.250
  Chirality :  0.047   0.223   1960
  Planarity :  0.003   0.033   2250
  Dihedral  :  9.725  68.966   1925
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 10.11 %
    Favored  : 86.98 %
  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:  0.07 (0.23), residues: 1525
  helix:  1.97 (0.23), residues: 520
  sheet:  0.86 (0.28), residues: 395
  loop : -2.38 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 206 
 HIS   0.002   0.000   HIS E 177 
 PHE   0.012   0.001   PHE D 236 
 TYR   0.014   0.001   TYR B 245 
 ARG   0.008   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03089 (  560)
  hydrogen bonds       : angle       3.96581 ( 1650)
  covalent geometry    : bond        0.00230 (13130)
  covalent geometry    : angle       0.49118 (17825)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 138
  time to evaluate  : 1.345 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8250 (t0) cc_final: 0.7531 (t70)
REVERT: B   65 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7394 (mtm180)
REVERT: B   86 ASP cc_start: 0.8104 (t0) cc_final: 0.7605 (t70)
REVERT: B  148 TYR cc_start: 0.9145 (m-80) cc_final: 0.8804 (m-80)
REVERT: C   86 ASP cc_start: 0.8193 (t0) cc_final: 0.7776 (t70)
REVERT: C  162 ILE cc_start: 0.8489 (mm) cc_final: 0.8126 (mm)
REVERT: C  174 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7706 (ttm-80)
REVERT: C  245 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6959 (t80)
REVERT: D   30 GLU cc_start: 0.6567 (tp30) cc_final: 0.5228 (tt0)
REVERT: D   65 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7674 (mtp-110)
REVERT: D   86 ASP cc_start: 0.8120 (t0) cc_final: 0.7596 (t70)
REVERT: D  174 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7698 (ttt-90)
REVERT: D  263 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7206 (m-30)
REVERT: E   65 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.7162 (mtm180)
REVERT: E  113 ASP cc_start: 0.7667 (m-30) cc_final: 0.7364 (p0)
REVERT: E  174 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7905 (mtp85)
REVERT: E  245 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6382 (t80)
REVERT: E  263 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7386 (m-30)
REVERT: E  265 MET cc_start: 0.8032 (mtp) cc_final: 0.7742 (mtp)
  outliers start: 40
  outliers final: 29
  residues processed: 162
  average time/residue: 0.2629
  time to fit residues: 60.8779
Evaluate side-chains
  162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  263 ASP
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 121 optimal weight:    7.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.152200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.109491 restraints weight = 13148.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.59
r_work: 0.2933 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13130  Z= 0.244
  Angle     :  0.608   6.111  17825  Z= 0.313
  Chirality :  0.052   0.217   1960
  Planarity :  0.004   0.035   2250
  Dihedral  : 10.333  83.165   1925
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 10.55 %
    Favored  : 86.69 %
  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: -0.05 (0.23), residues: 1525
  helix:  1.76 (0.23), residues: 530
  sheet:  1.02 (0.30), residues: 345
  loop : -2.30 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 206 
 HIS   0.004   0.001   HIS E 177 
 PHE   0.015   0.002   PHE D 236 
 TYR   0.026   0.002   TYR D 203 
 ARG   0.008   0.001   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04055 (  560)
  hydrogen bonds       : angle       4.26035 ( 1650)
  covalent geometry    : bond        0.00607 (13130)
  covalent geometry    : angle       0.60818 (17825)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6418.53 seconds
wall clock time: 111 minutes 40.51 seconds (6700.51 seconds total)