Starting phenix.real_space_refine
on Wed Mar  4 10:13:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d66_27218/03_2026/8d66_27218_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d66_27218/03_2026/8d66_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d66_27218/03_2026/8d66_27218_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d66_27218/03_2026/8d66_27218_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d66_27218/03_2026/8d66_27218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d66_27218/03_2026/8d66_27218.map"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 1.82, per 1000 atoms: 0.14
  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: 0.97
  Conformation dependent library (CDL) restraints added in 579.5 milliseconds
  

  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: 0.37
  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: 1.83

  Time building geometry restraints manager: 1.32 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.820
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.870
-------------------------------------------------------------------------------
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 : 7.73
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.001   ARG B  91 
 TYR   0.023   0.003   TYR D 245 
 PHE   0.016   0.002   PHE D 228 
 TRP   0.038   0.003   TRP C 206 
 HIS   0.004   0.002   HIS A 177 

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

*********************** 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  : 0.402 
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: 0.7627 (mtp-110) cc_final: 0.7151 (mtm180)
REVERT: B   86 ASP cc_start: 0.7811 (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: 0.7060 (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: 0.8132 (mtpp)
REVERT: E   86 ASP cc_start: 0.7911 (t0) cc_final: 0.7397 (t70)
REVERT: E  113 ASP cc_start: 0.7199 (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: 0.1312
  time to fit residues: 29.0248
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  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0020
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0970
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.0010
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    0.3192

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.160504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.116710 restraints weight = 13201.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.68
r_work: 0.3082 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  13130  Z= 0.108
  Angle     :  0.538   5.213  17825  Z= 0.273
  Chirality :  0.047   0.184   1960
  Planarity :  0.004   0.035   2250
  Dihedral  : 14.752  92.883   1925
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  4.95 %
    Favored  : 93.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.22), residues: 1525
  helix:  0.94 (0.24), residues: 515
  sheet:  0.67 (0.28), residues: 395
  loop : -2.58 (0.22), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 174 
 TYR   0.014   0.001   TYR B 245 
 PHE   0.010   0.001   PHE D 236 
 TRP   0.011   0.001   TRP A 206 
 HIS   0.001   0.000   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (13130)
  covalent geometry    : angle       0.53834 (17825)
  hydrogen bonds       : bond        0.03481 (  560)
  hydrogen bonds       : angle       4.52020 ( 1650)

*********************** 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
  162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.9125 (mttt) cc_final: 0.8814 (mtmt)
REVERT: A   86 ASP cc_start: 0.8287 (t0) cc_final: 0.7737 (t70)
REVERT: A  223 PHE cc_start: 0.8444 (m-80) cc_final: 0.7815 (m-80)
REVERT: A  245 TYR cc_start: 0.7992 (m-80) cc_final: 0.7392 (m-80)
REVERT: B   30 GLU cc_start: 0.5853 (tt0) cc_final: 0.5648 (tt0)
REVERT: B   54 LYS cc_start: 0.8806 (mttt) cc_final: 0.8119 (mmmt)
REVERT: B   65 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7692 (mtm180)
REVERT: B   86 ASP cc_start: 0.8207 (t0) cc_final: 0.7767 (t70)
REVERT: C   30 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6756 (tp30)
REVERT: C  114 MET cc_start: 0.9048 (mtt) cc_final: 0.8709 (mtt)
REVERT: C  265 MET cc_start: 0.8633 (mtp) cc_final: 0.8275 (mtp)
REVERT: D   86 ASP cc_start: 0.8138 (t0) cc_final: 0.7567 (t70)
REVERT: D  113 ASP cc_start: 0.8056 (m-30) cc_final: 0.7472 (p0)
REVERT: E   21 ASN cc_start: 0.8757 (t0) cc_final: 0.8554 (t0)
REVERT: E   86 ASP cc_start: 0.8281 (t0) cc_final: 0.7887 (t70)
REVERT: E  113 ASP cc_start: 0.7938 (m-30) cc_final: 0.7233 (p0)
REVERT: E  114 MET cc_start: 0.9268 (mtt) cc_final: 0.8870 (mtt)
REVERT: E  174 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8186 (ttm-80)
  outliers start: 15
  outliers final: 10
  residues processed: 153
  average time/residue: 0.1184
  time to fit residues: 25.7762
Evaluate side-chains
  131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
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  278 LEU
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C 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 35 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0470
   chunk 130 optimal weight:    7.9990
   chunk 147 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   chunk 104 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0070
   overall best weight:    0.8098

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.160019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.120315 restraints weight = 13216.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.60
r_work: 0.3165 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13130  Z= 0.108
  Angle     :  0.502   5.132  17825  Z= 0.255
  Chirality :  0.047   0.208   1960
  Planarity :  0.003   0.027   2250
  Dihedral  : 12.306  82.538   1925
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  6.98 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.23), residues: 1525
  helix:  1.28 (0.24), residues: 530
  sheet:  0.87 (0.28), residues: 395
  loop : -2.23 (0.23), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 174 
 TYR   0.013   0.001   TYR C 245 
 PHE   0.008   0.001   PHE E 236 
 TRP   0.015   0.001   TRP C 206 
 HIS   0.002   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (13130)
  covalent geometry    : angle       0.50198 (17825)
  hydrogen bonds       : bond        0.03273 (  560)
  hydrogen bonds       : angle       4.18612 ( 1650)

*********************** 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
  162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8314 (t0) cc_final: 0.7737 (t70)
REVERT: B   54 LYS cc_start: 0.8762 (mttt) cc_final: 0.8102 (mmmt)
REVERT: B   65 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7687 (mtm180)
REVERT: B   86 ASP cc_start: 0.8165 (t0) cc_final: 0.7722 (t70)
REVERT: C  174 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7869 (ttm-80)
REVERT: C  245 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7560 (t80)
REVERT: C  270 TYR cc_start: 0.8506 (m-80) cc_final: 0.8286 (m-80)
REVERT: D   86 ASP cc_start: 0.8187 (t0) cc_final: 0.7574 (t70)
REVERT: D  113 ASP cc_start: 0.8020 (m-30) cc_final: 0.7474 (p0)
REVERT: D  174 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.7996 (mtp85)
REVERT: D  245 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7491 (t80)
REVERT: E   21 ASN cc_start: 0.8769 (t0) cc_final: 0.8531 (t0)
REVERT: E  113 ASP cc_start: 0.8027 (m-30) cc_final: 0.7522 (p0)
REVERT: E  114 MET cc_start: 0.9306 (mtt) cc_final: 0.8936 (mtt)
REVERT: E  245 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6816 (t80)
  outliers start: 24
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1169
  time to fit residues: 25.3195
Evaluate side-chains
  142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
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  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  245 TYR
Chi-restraints excluded: chain E residue  259 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0770
   chunk 86 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0970
   chunk 78 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 134 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 16 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
C 124 GLN
D  27 ASN
D 124 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.161165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.121492 restraints weight = 13161.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.56
r_work: 0.3065 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13130  Z= 0.098
  Angle     :  0.483   5.632  17825  Z= 0.245
  Chirality :  0.046   0.214   1960
  Planarity :  0.003   0.029   2250
  Dihedral  : 11.264  74.725   1925
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  7.64 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.23), residues: 1525
  helix:  1.59 (0.23), residues: 525
  sheet:  0.97 (0.28), residues: 395
  loop : -2.24 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 123 
 TYR   0.012   0.001   TYR B 245 
 PHE   0.017   0.001   PHE B 236 
 TRP   0.021   0.001   TRP B 206 
 HIS   0.001   0.000   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (13130)
  covalent geometry    : angle       0.48287 (17825)
  hydrogen bonds       : bond        0.03061 (  560)
  hydrogen bonds       : angle       4.02366 ( 1650)

*********************** 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
  163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8288 (t0) cc_final: 0.7618 (t70)
REVERT: A  137 ASN cc_start: 0.8647 (p0) cc_final: 0.8436 (p0)
REVERT: B   54 LYS cc_start: 0.8580 (mttt) cc_final: 0.7782 (mmmt)
REVERT: B   65 ARG cc_start: 0.7856 (mtp-110) cc_final: 0.7315 (mtm180)
REVERT: B   86 ASP cc_start: 0.8104 (t0) cc_final: 0.7626 (t70)
REVERT: B  123 ARG cc_start: 0.7982 (ttt-90) cc_final: 0.7736 (ttm-80)
REVERT: C   34 LYS cc_start: 0.9076 (mttt) cc_final: 0.8828 (mttp)
REVERT: C  174 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7479 (mtp180)
REVERT: C  245 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7271 (t80)
REVERT: D   86 ASP cc_start: 0.8130 (t0) cc_final: 0.7653 (t70)
REVERT: D  162 ILE cc_start: 0.8371 (mm) cc_final: 0.8017 (mm)
REVERT: D  174 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7827 (mtp85)
REVERT: D  245 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.7178 (t80)
REVERT: E   65 ARG cc_start: 0.7626 (mtp-110) cc_final: 0.7268 (mtm180)
REVERT: E  113 ASP cc_start: 0.7888 (m-30) cc_final: 0.7243 (p0)
REVERT: E  245 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6453 (t80)
  outliers start: 26
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1210
  time to fit residues: 26.1164
Evaluate side-chains
  149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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 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  245 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  278 LEU
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  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  259 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 141 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0170
   chunk 140 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 109 optimal weight:    0.8980
   chunk 133 optimal weight:    3.9990
   overall best weight:    1.1020

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
D  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.159473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.115360 restraints weight = 13252.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.66
r_work: 0.3029 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13130  Z= 0.116
  Angle     :  0.496   5.214  17825  Z= 0.252
  Chirality :  0.047   0.214   1960
  Planarity :  0.003   0.032   2250
  Dihedral  : 10.746  73.798   1925
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  8.15 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.23), residues: 1525
  helix:  1.79 (0.23), residues: 525
  sheet:  0.98 (0.28), residues: 395
  loop : -2.23 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 174 
 TYR   0.014   0.001   TYR C 245 
 PHE   0.009   0.001   PHE A 236 
 TRP   0.013   0.001   TRP B 206 
 HIS   0.002   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (13130)
  covalent geometry    : angle       0.49552 (17825)
  hydrogen bonds       : bond        0.03222 (  560)
  hydrogen bonds       : angle       3.99551 ( 1650)

*********************** 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
  157 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A   86 ASP cc_start: 0.8188 (t0) cc_final: 0.7478 (t70)
REVERT: B   54 LYS cc_start: 0.8608 (mttt) cc_final: 0.8321 (mttp)
REVERT: B   65 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7481 (mtm180)
REVERT: B   86 ASP cc_start: 0.8101 (t0) cc_final: 0.7594 (t70)
REVERT: C   34 LYS cc_start: 0.9129 (mttt) cc_final: 0.8875 (mttp)
REVERT: C  174 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7485 (mtp180)
REVERT: C  245 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.7093 (t80)
REVERT: C  255 ARG cc_start: 0.7486 (ptp-170) cc_final: 0.6915 (ptp-170)
REVERT: D   86 ASP cc_start: 0.8140 (t0) cc_final: 0.7622 (t70)
REVERT: D  162 ILE cc_start: 0.8288 (mm) cc_final: 0.7939 (mm)
REVERT: D  174 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7883 (mtp85)
REVERT: D  245 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.7122 (t80)
REVERT: E   65 ARG cc_start: 0.7528 (mtp-110) cc_final: 0.7145 (mtm180)
REVERT: E  113 ASP cc_start: 0.7945 (m-30) cc_final: 0.7224 (p0)
REVERT: E  245 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6346 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 145
  average time/residue: 0.1173
  time to fit residues: 24.4221
Evaluate side-chains
  144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
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 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  245 TYR
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  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  259 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 102 optimal weight:    4.9990
   chunk 43 optimal weight:    0.3980
   chunk 2 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 113 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   overall best weight:    2.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
D  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.155293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.115655 restraints weight = 13227.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.64
r_work: 0.2973 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13130  Z= 0.186
  Angle     :  0.565   5.196  17825  Z= 0.290
  Chirality :  0.050   0.208   1960
  Planarity :  0.004   0.033   2250
  Dihedral  : 10.927  82.322   1925
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  8.58 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.23), residues: 1525
  helix:  1.80 (0.23), residues: 530
  sheet:  0.78 (0.28), residues: 395
  loop : -2.23 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  91 
 TYR   0.019   0.002   TYR D 245 
 PHE   0.019   0.002   PHE B 236 
 TRP   0.016   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (13130)
  covalent geometry    : angle       0.56450 (17825)
  hydrogen bonds       : bond        0.03793 (  560)
  hydrogen bonds       : angle       4.18366 ( 1650)

*********************** 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
  158 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.8967 (mttt) cc_final: 0.8633 (mtmt)
REVERT: A  245 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7488 (m-80)
REVERT: B   54 LYS cc_start: 0.8609 (mttt) cc_final: 0.8308 (mtmt)
REVERT: B   65 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7596 (mtm180)
REVERT: B   86 ASP cc_start: 0.8169 (t0) cc_final: 0.7684 (t70)
REVERT: C   34 LYS cc_start: 0.9198 (mttt) cc_final: 0.8960 (mttp)
REVERT: C  245 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: D   30 GLU cc_start: 0.6757 (tp30) cc_final: 0.5367 (tt0)
REVERT: D   65 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7677 (mtm180)
REVERT: D   86 ASP cc_start: 0.8129 (t0) cc_final: 0.7624 (t70)
REVERT: D  174 ARG cc_start: 0.8058 (ttt-90) cc_final: 0.7777 (mtp85)
REVERT: D  245 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7101 (t80)
REVERT: E   65 ARG cc_start: 0.7754 (mtp-110) cc_final: 0.7389 (mtm180)
REVERT: E  113 ASP cc_start: 0.7856 (m-30) cc_final: 0.7228 (p0)
REVERT: E  245 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6272 (t80)
  outliers start: 32
  outliers final: 23
  residues processed: 145
  average time/residue: 0.1175
  time to fit residues: 24.1315
Evaluate side-chains
  147 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
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 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  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  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  180 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 27 optimal weight:   20.0000
   chunk 105 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 122 optimal weight:    4.9990
   overall best weight:    1.7988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.156037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.115484 restraints weight = 13160.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.53
r_work: 0.2994 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13130  Z= 0.153
  Angle     :  0.537   5.444  17825  Z= 0.275
  Chirality :  0.049   0.211   1960
  Planarity :  0.003   0.033   2250
  Dihedral  : 10.671  80.989   1925
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  :  9.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.23), residues: 1525
  helix:  1.79 (0.23), residues: 530
  sheet:  0.76 (0.28), residues: 395
  loop : -2.23 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  65 
 TYR   0.017   0.001   TYR D 245 
 PHE   0.013   0.001   PHE C 236 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13130)
  covalent geometry    : angle       0.53675 (17825)
  hydrogen bonds       : bond        0.03588 (  560)
  hydrogen bonds       : angle       4.13428 ( 1650)

*********************** 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
  158 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 119
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.8909 (mttt) cc_final: 0.8594 (mtmt)
REVERT: B   54 LYS cc_start: 0.8626 (mttt) cc_final: 0.8342 (mtmt)
REVERT: B   65 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7463 (mtm180)
REVERT: B   86 ASP cc_start: 0.8163 (t0) cc_final: 0.7677 (t70)
REVERT: C   34 LYS cc_start: 0.9194 (mttt) cc_final: 0.8962 (mttp)
REVERT: C  174 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7691 (ttm-80)
REVERT: C  245 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7265 (t80)
REVERT: D   30 GLU cc_start: 0.6630 (tp30) cc_final: 0.5284 (tt0)
REVERT: D   65 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7739 (mtm180)
REVERT: D   86 ASP cc_start: 0.8168 (t0) cc_final: 0.7702 (t70)
REVERT: D  174 ARG cc_start: 0.8091 (ttt-90) cc_final: 0.7828 (mtp85)
REVERT: D  245 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.7213 (t80)
REVERT: E   65 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7398 (mtm180)
REVERT: E  113 ASP cc_start: 0.7794 (m-30) cc_final: 0.7281 (p0)
REVERT: E  245 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6329 (t80)
  outliers start: 39
  outliers final: 29
  residues processed: 146
  average time/residue: 0.1210
  time to fit residues: 25.1502
Evaluate side-chains
  143 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
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   61 THR
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  278 LEU
Chi-restraints excluded: chain C residue   30 GLU
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0980
   chunk 76 optimal weight:    0.5980
   chunk 138 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
A 177 HIS
D  27 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.159482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.119984 restraints weight = 13055.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.61
r_work: 0.3196 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13130  Z= 0.103
  Angle     :  0.489   6.595  17825  Z= 0.248
  Chirality :  0.047   0.214   1960
  Planarity :  0.003   0.032   2250
  Dihedral  : 10.055  71.648   1925
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  9.67 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.23), residues: 1525
  helix:  1.93 (0.23), residues: 525
  sheet:  0.88 (0.28), residues: 395
  loop : -2.27 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  65 
 TYR   0.013   0.001   TYR B 245 
 PHE   0.009   0.001   PHE E 236 
 TRP   0.016   0.001   TRP D 206 
 HIS   0.002   0.000   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (13130)
  covalent geometry    : angle       0.48922 (17825)
  hydrogen bonds       : bond        0.03176 (  560)
  hydrogen bonds       : angle       3.95030 ( 1650)

*********************** 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
  167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.462 
Fit side-chains
REVERT: B   54 LYS cc_start: 0.8603 (mttt) cc_final: 0.8361 (mttp)
REVERT: B   65 ARG cc_start: 0.8080 (mtp-110) cc_final: 0.7649 (mtm180)
REVERT: B   86 ASP cc_start: 0.8005 (t0) cc_final: 0.7567 (t70)
REVERT: B  148 TYR cc_start: 0.9097 (m-80) cc_final: 0.8864 (m-80)
REVERT: C   86 ASP cc_start: 0.8166 (t0) cc_final: 0.7817 (t70)
REVERT: C  174 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7784 (mtp85)
REVERT: C  245 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7396 (t80)
REVERT: C  252 ILE cc_start: 0.7996 (mm) cc_final: 0.7605 (pt)
REVERT: D   86 ASP cc_start: 0.8061 (t0) cc_final: 0.7581 (t70)
REVERT: D  162 ILE cc_start: 0.8669 (mm) cc_final: 0.8374 (mm)
REVERT: D  174 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.7901 (mtp85)
REVERT: D  245 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7554 (t80)
REVERT: E   65 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7516 (mtm180)
REVERT: E  113 ASP cc_start: 0.7701 (m-30) cc_final: 0.7477 (p0)
REVERT: E  245 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6810 (t80)
  outliers start: 34
  outliers final: 24
  residues processed: 156
  average time/residue: 0.1183
  time to fit residues: 26.6791
Evaluate side-chains
  148 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 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  145 ILE
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  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  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 7 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 134 optimal weight:    0.0070
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 6 optimal weight:    0.2980
   chunk 62 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.0402

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
D  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.158916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.118324 restraints weight = 13107.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.52
r_work: 0.3034 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2294

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= 0.113
  Angle     :  0.494   5.140  17825  Z= 0.253
  Chirality :  0.047   0.214   1960
  Planarity :  0.003   0.032   2250
  Dihedral  :  9.898  69.577   1925
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.04 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.23), residues: 1525
  helix:  1.99 (0.23), residues: 525
  sheet:  0.95 (0.28), residues: 395
  loop : -2.25 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  65 
 TYR   0.014   0.001   TYR D 245 
 PHE   0.010   0.001   PHE A 236 
 TRP   0.022   0.001   TRP E 206 
 HIS   0.002   0.000   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (13130)
  covalent geometry    : angle       0.49357 (17825)
  hydrogen bonds       : bond        0.03268 (  560)
  hydrogen bonds       : angle       3.94009 ( 1650)

*********************** 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
  155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.415 
Fit side-chains
REVERT: B   54 LYS cc_start: 0.8587 (mttt) cc_final: 0.8309 (mttp)
REVERT: B   65 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7547 (mtm180)
REVERT: B   86 ASP cc_start: 0.8148 (t0) cc_final: 0.7665 (t70)
REVERT: B  148 TYR cc_start: 0.9119 (m-80) cc_final: 0.8800 (m-80)
REVERT: C   86 ASP cc_start: 0.8211 (t0) cc_final: 0.7808 (t70)
REVERT: C  174 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7625 (mtp85)
REVERT: C  245 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7226 (t80)
REVERT: D   86 ASP cc_start: 0.8118 (t0) cc_final: 0.7589 (t70)
REVERT: D  162 ILE cc_start: 0.8382 (mm) cc_final: 0.7827 (mm)
REVERT: D  174 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7843 (mtp85)
REVERT: D  245 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7235 (t80)
REVERT: E   65 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.7170 (mtm180)
REVERT: E  113 ASP cc_start: 0.7731 (m-30) cc_final: 0.7257 (p0)
REVERT: E  245 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6421 (t80)
  outliers start: 30
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1240
  time to fit residues: 25.5914
Evaluate side-chains
  151 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
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 B residue   61 THR
Chi-restraints excluded: chain B residue  145 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  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  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  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  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 33 optimal weight:    0.8980
   chunk 58 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 141 optimal weight:    9.9990
   chunk 31 optimal weight:    0.2980
   chunk 134 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
A 182 GLN
D  27 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.172273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.129241 restraints weight = 13046.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.43
r_work: 0.3131 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13130  Z= 0.189
  Angle     :  0.569   5.306  17825  Z= 0.293
  Chirality :  0.050   0.212   1960
  Planarity :  0.004   0.034   2250
  Dihedral  : 10.248  78.241   1925
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.04 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.23), residues: 1525
  helix:  1.89 (0.23), residues: 530
  sheet:  1.11 (0.30), residues: 345
  loop : -2.19 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  65 
 TYR   0.019   0.002   TYR D 245 
 PHE   0.014   0.002   PHE A 236 
 TRP   0.026   0.002   TRP C 206 
 HIS   0.003   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (13130)
  covalent geometry    : angle       0.56854 (17825)
  hydrogen bonds       : bond        0.03849 (  560)
  hydrogen bonds       : angle       4.14765 ( 1650)

********************** 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
  159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 124
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   54 LYS cc_start: 0.9027 (mttt) cc_final: 0.8746 (mtmt)
REVERT: B   54 LYS cc_start: 0.8695 (mttt) cc_final: 0.8431 (mtmt)
REVERT: B   65 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7895 (mtm180)
REVERT: B   86 ASP cc_start: 0.8245 (t0) cc_final: 0.7766 (t70)
REVERT: B  174 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8081 (ttt-90)
REVERT: C  245 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7576 (t80)
REVERT: D   30 GLU cc_start: 0.6849 (tp30) cc_final: 0.5983 (tp30)
REVERT: D   86 ASP cc_start: 0.8239 (t0) cc_final: 0.7683 (t70)
REVERT: D  162 ILE cc_start: 0.8904 (mm) cc_final: 0.8516 (mm)
REVERT: D  245 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7541 (t80)
REVERT: E   65 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7671 (mtm180)
REVERT: E  245 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.6725 (t80)
  outliers start: 35
  outliers final: 29
  residues processed: 146
  average time/residue: 0.1225
  time to fit residues: 25.4094
Evaluate side-chains
  148 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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 B residue   61 THR
Chi-restraints excluded: chain B residue  145 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  145 ILE
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  227 SER
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  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 76 optimal weight:    4.9990
   chunk 146 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 128 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.154710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.114184 restraints weight = 13170.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.66
r_work: 0.3116 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13130  Z= 0.186
  Angle     :  0.568   5.399  17825  Z= 0.295
  Chirality :  0.050   0.213   1960
  Planarity :  0.004   0.033   2250
  Dihedral  : 10.238  79.819   1925
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.40 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.23), residues: 1525
  helix:  1.86 (0.23), residues: 530
  sheet:  1.04 (0.30), residues: 345
  loop : -2.22 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  65 
 TYR   0.017   0.002   TYR D 245 
 PHE   0.014   0.002   PHE E 236 
 TRP   0.020   0.001   TRP A 206 
 HIS   0.003   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (13130)
  covalent geometry    : angle       0.56793 (17825)
  hydrogen bonds       : bond        0.03801 (  560)
  hydrogen bonds       : angle       4.13754 ( 1650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2979.51 seconds
wall clock time: 51 minutes 33.51 seconds (3093.51 seconds total)