Starting phenix.real_space_refine
on Wed Jul 30 17:50:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ngc_49382/07_2025/9ngc_49382_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ngc_49382/07_2025/9ngc_49382.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ngc_49382/07_2025/9ngc_49382.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ngc_49382/07_2025/9ngc_49382.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ngc_49382/07_2025/9ngc_49382_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ngc_49382/07_2025/9ngc_49382_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.131
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
     S      25      5.16       5
     Na      2      4.78       5
     C    8305      2.51       5
     N    2115      2.21       5
     O    2275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12722
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2540
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 13, 'TRANS': 296}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 6
          Unusual residues: {' NA': 2, '3CN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 5.88, per 1000 atoms: 0.46
  Number of scatterers: 12722
  At special positions: 0
  Unit cell: (91.14, 93.744, 124.992, 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      25     16.00
     Na      2     11.00
     O    2275      8.00
     N    2115      7.00
     C    8305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.91
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2930

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 20 sheets defined
      36.8% alpha, 41.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.842A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 222
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 286
    Processing helix  chain 'A' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG A 301 " --> pdb=" O   GLN A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 301'
    Processing helix  chain 'A' and resid 302 through 320
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.842A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 222
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'B' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN B 251 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 286
    Processing helix  chain 'B' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG B 301 " --> pdb=" O   GLN B 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 301'
    Processing helix  chain 'B' and resid 302 through 320
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.842A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 222
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'C' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER C 235 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN C 251 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE C 252 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 286
    Processing helix  chain 'C' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG C 301 " --> pdb=" O   GLN C 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 298 through 301'
    Processing helix  chain 'C' and resid 302 through 320
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.843A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 222
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing helix  chain 'D' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR D 234 " --> pdb=" O   GLU D 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER D 235 " --> pdb=" O   ARG D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 253
      removed outlier: 3.634A  pdb=" N   ASN D 251 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE D 252 " --> pdb=" O   TYR D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 286
    Processing helix  chain 'D' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG D 301 " --> pdb=" O   GLN D 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 298 through 301'
    Processing helix  chain 'D' and resid 302 through 320
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.843A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 222
    Processing helix  chain 'E' and resid 223 through 225
      No H-bonds generated for 'chain 'E' and resid 223 through 225'
    Processing helix  chain 'E' and resid 227 through 244
      removed outlier: 3.627A  pdb=" N   THR E 234 " --> pdb=" O   GLU E 230 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER E 235 " --> pdb=" O   ARG E 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 247 through 253
      removed outlier: 3.635A  pdb=" N   ASN E 251 " --> pdb=" O   PHE E 247 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE E 252 " --> pdb=" O   TYR E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 286
    Processing helix  chain 'E' and resid 298 through 301
      removed outlier: 4.183A  pdb=" N   ARG E 301 " --> pdb=" O   GLN E 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 298 through 301'
    Processing helix  chain 'E' and resid 302 through 320
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.364A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.364A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.364A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.364A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.363A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58
      removed outlier: 3.575A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.745A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    690 hydrogen bonds defined for protein.
    1995 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: 4.10

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3688
        1.34 -     1.45: 2308
        1.45 -     1.57: 7019
        1.57 -     1.69: 5
        1.69 -     1.80: 45
  Bond restraints: 13065
  Sorted by residual:
  bond pdb=" C   PHE D 304 "
       pdb=" N   PRO D 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.18e+00
  bond pdb=" C   PHE E 304 "
       pdb=" N   PRO E 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.17e+00
  bond pdb=" C   PHE A 304 "
       pdb=" N   PRO A 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.15e+00
  bond pdb=" C   PHE B 304 "
       pdb=" N   PRO B 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.13e+00
  bond pdb=" C   PHE C 304 "
       pdb=" N   PRO C 305 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.018 1.23e-02 6.61e+03 2.11e+00
  ... (remaining 13060 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 17044
        1.53 -     3.05: 576
        3.05 -     4.58: 95
        4.58 -     6.11: 35
        6.11 -     7.63: 30
  Bond angle restraints: 17780
  Sorted by residual:
  angle pdb=" C   ASN B  60 "
        pdb=" N   THR B  61 "
        pdb=" CA  THR B  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.17   -7.63 1.91e+00 2.74e-01 1.60e+01
  angle pdb=" C   ASN A  60 "
        pdb=" N   THR A  61 "
        pdb=" CA  THR A  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.12   -7.58 1.91e+00 2.74e-01 1.57e+01
  angle pdb=" C   ASN C  60 "
        pdb=" N   THR C  61 "
        pdb=" CA  THR C  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.11   -7.57 1.91e+00 2.74e-01 1.57e+01
  angle pdb=" C   ASN E  60 "
        pdb=" N   THR E  61 "
        pdb=" CA  THR E  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.09   -7.55 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" C   ASN D  60 "
        pdb=" N   THR D  61 "
        pdb=" CA  THR D  61 "
      ideal   model   delta    sigma   weight residual
     121.54  129.08   -7.54 1.91e+00 2.74e-01 1.56e+01
  ... (remaining 17775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.15: 6517
       12.15 -    24.29: 808
       24.29 -    36.44: 210
       36.44 -    48.59: 60
       48.59 -    60.73: 10
  Dihedral angle restraints: 7605
    sinusoidal: 3060
      harmonic: 4545
  Sorted by residual:
  dihedral pdb=" CA  ILE D 157 "
           pdb=" C   ILE D 157 "
           pdb=" N   ASP D 158 "
           pdb=" CA  ASP D 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.94  -23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  ILE A 157 "
           pdb=" C   ILE A 157 "
           pdb=" N   ASP A 158 "
           pdb=" CA  ASP A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  ILE C 157 "
           pdb=" C   ILE C 157 "
           pdb=" N   ASP C 158 "
           pdb=" CA  ASP C 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 7602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1428
       0.049 -    0.097: 373
       0.097 -    0.146: 134
       0.146 -    0.194: 15
       0.194 -    0.243: 5
  Chirality restraints: 1955
  Sorted by residual:
  chirality pdb=" CB  THR B 149 "
            pdb=" CA  THR B 149 "
            pdb=" OG1 THR B 149 "
            pdb=" CG2 THR B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CB  THR A 149 "
            pdb=" CA  THR A 149 "
            pdb=" OG1 THR A 149 "
            pdb=" CG2 THR A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CB  THR E 149 "
            pdb=" CA  THR E 149 "
            pdb=" OG1 THR E 149 "
            pdb=" CG2 THR E 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1952 not shown)

  Planarity restraints: 2265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  54 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.04e+00
        pdb=" N   PRO B  55 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B  55 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  55 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  54 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO A  55 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A  55 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  55 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E  54 "    0.033 5.00e-02 4.00e+02   5.02e-02 4.02e+00
        pdb=" N   PRO E  55 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO E  55 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E  55 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2262 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1811
        2.76 -     3.30: 11025
        3.30 -     3.83: 20891
        3.83 -     4.37: 24391
        4.37 -     4.90: 43952
  Nonbonded interactions: 102070
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 229 "
            pdb=" OE2 GLU E 230 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER C 229 "
            pdb=" OE2 GLU D 230 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG  SER A 229 "
            pdb=" OE2 GLU B 230 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE2 GLU A 230 "
            pdb=" OG  SER E 229 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER B 229 "
            pdb=" OE2 GLU C 230 "
     model   vdw
     2.265 3.040
  ... (remaining 102065 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 11 through 320 or resid 401))
  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:             1.630
  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:          0.490
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     28.440
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13065  Z= 0.185
  Angle     :  0.728   7.632  17780  Z= 0.381
  Chirality :  0.050   0.243   1955
  Planarity :  0.005   0.050   2265
  Dihedral  : 11.953  60.734   4675
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.21), residues: 1540
  helix: -0.60 (0.20), residues: 565
  sheet:  1.40 (0.25), residues: 465
  loop : -2.16 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 206 
 HIS   0.004   0.001   HIS B 177 
 PHE   0.011   0.002   PHE E 116 
 TYR   0.009   0.001   TYR B 203 
 ARG   0.005   0.001   ARG C  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15258 (  600)
  hydrogen bonds       : angle       6.85309 ( 1995)
  covalent geometry    : bond        0.00413 (13065)
  covalent geometry    : angle       0.72810 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.427 
Fit side-chains
REVERT: A   36 ASP cc_start: 0.8021 (t0) cc_final: 0.7726 (t70)
REVERT: A  155 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6675 (mm-30)
REVERT: A  176 ASP cc_start: 0.7778 (m-30) cc_final: 0.7555 (m-30)
REVERT: A  187 GLU cc_start: 0.7446 (tt0) cc_final: 0.7181 (tt0)
REVERT: B   34 LYS cc_start: 0.8301 (mttm) cc_final: 0.8091 (mttp)
REVERT: B   36 ASP cc_start: 0.8020 (t0) cc_final: 0.7656 (t70)
REVERT: B   61 THR cc_start: 0.8208 (t) cc_final: 0.7807 (p)
REVERT: B   69 ASN cc_start: 0.7815 (m-40) cc_final: 0.7601 (m-40)
REVERT: B   90 LYS cc_start: 0.8336 (pttt) cc_final: 0.7839 (ptpp)
REVERT: B  155 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6692 (mm-30)
REVERT: C   27 ASN cc_start: 0.8271 (t0) cc_final: 0.8044 (t0)
REVERT: C   36 ASP cc_start: 0.8036 (t0) cc_final: 0.7614 (t0)
REVERT: C   61 THR cc_start: 0.8176 (t) cc_final: 0.7742 (p)
REVERT: C   90 LYS cc_start: 0.8308 (pttt) cc_final: 0.7826 (ptpp)
REVERT: C  155 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6665 (mm-30)
REVERT: C  187 GLU cc_start: 0.7660 (tt0) cc_final: 0.7405 (tt0)
REVERT: C  233 GLN cc_start: 0.6719 (pt0) cc_final: 0.6490 (pt0)
REVERT: D   34 LYS cc_start: 0.8255 (mttm) cc_final: 0.8024 (mttp)
REVERT: D   36 ASP cc_start: 0.8108 (t0) cc_final: 0.7886 (t70)
REVERT: D   90 LYS cc_start: 0.8440 (pttt) cc_final: 0.7937 (ptpp)
REVERT: D  150 GLU cc_start: 0.7664 (pm20) cc_final: 0.7405 (mp0)
REVERT: D  155 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6711 (mm-30)
REVERT: D  176 ASP cc_start: 0.7708 (m-30) cc_final: 0.7425 (m-30)
REVERT: D  233 GLN cc_start: 0.6844 (pt0) cc_final: 0.6618 (pt0)
REVERT: E   36 ASP cc_start: 0.7960 (t0) cc_final: 0.7660 (t70)
REVERT: E   61 THR cc_start: 0.8127 (t) cc_final: 0.7689 (p)
REVERT: E  155 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6632 (mm-30)
REVERT: E  233 GLN cc_start: 0.7002 (pt0) cc_final: 0.6725 (pt0)
REVERT: E  239 MET cc_start: 0.7824 (ttp) cc_final: 0.7565 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 1.3409
  time to fit residues: 273.7595
Evaluate side-chains
  140 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    0.5980
   chunk 117 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 140 optimal weight:    4.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 184 ASN
B  27 ASN
B 146 GLN
E  27 ASN
E  42 GLN
E 146 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.150055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.117790 restraints weight = 14254.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.13
r_work: 0.3318 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025  13065  Z= 0.189
  Angle     :  0.580   6.014  17780  Z= 0.307
  Chirality :  0.047   0.141   1955
  Planarity :  0.004   0.044   2265
  Dihedral  :  4.633  19.551   1715
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.87 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.22), residues: 1540
  helix:  0.40 (0.22), residues: 560
  sheet:  1.30 (0.26), residues: 465
  loop : -2.04 (0.24), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 206 
 HIS   0.005   0.001   HIS B 177 
 PHE   0.012   0.001   PHE B 116 
 TYR   0.009   0.001   TYR A 204 
 ARG   0.005   0.001   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03820 (  600)
  hydrogen bonds       : angle       4.78764 ( 1995)
  covalent geometry    : bond        0.00453 (13065)
  covalent geometry    : angle       0.57974 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 1.307 
Fit side-chains
REVERT: A   36 ASP cc_start: 0.8795 (t0) cc_final: 0.8576 (t70)
REVERT: A  150 GLU cc_start: 0.7833 (pm20) cc_final: 0.7462 (mp0)
REVERT: A  155 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6900 (mm-30)
REVERT: A  156 GLU cc_start: 0.7780 (tt0) cc_final: 0.7377 (tt0)
REVERT: A  176 ASP cc_start: 0.8017 (m-30) cc_final: 0.7694 (m-30)
REVERT: B   69 ASN cc_start: 0.7416 (m-40) cc_final: 0.7127 (m-40)
REVERT: B   90 LYS cc_start: 0.8355 (pttt) cc_final: 0.7887 (ptpp)
REVERT: B  150 GLU cc_start: 0.7777 (pm20) cc_final: 0.7295 (mp0)
REVERT: B  155 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6690 (mm-30)
REVERT: B  156 GLU cc_start: 0.7739 (tt0) cc_final: 0.7353 (tt0)
REVERT: C   36 ASP cc_start: 0.8780 (t0) cc_final: 0.8476 (t0)
REVERT: C   90 LYS cc_start: 0.8292 (pttt) cc_final: 0.7723 (ptpp)
REVERT: C  150 GLU cc_start: 0.7750 (pm20) cc_final: 0.7340 (mp0)
REVERT: C  155 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6845 (mm-30)
REVERT: D   27 ASN cc_start: 0.8176 (t0) cc_final: 0.7344 (t0)
REVERT: D   69 ASN cc_start: 0.7485 (m-40) cc_final: 0.7251 (m-40)
REVERT: D   90 LYS cc_start: 0.8414 (pttt) cc_final: 0.7807 (ptpp)
REVERT: D   93 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8281 (mtp)
REVERT: D  150 GLU cc_start: 0.7679 (pm20) cc_final: 0.7257 (mp0)
REVERT: D  155 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6967 (mm-30)
REVERT: D  176 ASP cc_start: 0.7912 (m-30) cc_final: 0.7582 (m-30)
REVERT: D  233 GLN cc_start: 0.6629 (pt0) cc_final: 0.6384 (tt0)
REVERT: E   36 ASP cc_start: 0.8676 (t0) cc_final: 0.8406 (t0)
REVERT: E   93 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8289 (mtp)
REVERT: E  155 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6957 (mm-30)
REVERT: E  174 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7629 (ttm-80)
  outliers start: 21
  outliers final: 6
  residues processed: 169
  average time/residue: 1.5937
  time to fit residues: 288.1505
Evaluate side-chains
  153 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 145
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 150 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 128 optimal weight:    0.0970
   chunk 91 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
A 233 GLN
B  27 ASN
E  27 ASN
E  42 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.152090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.118881 restraints weight = 14347.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.18
r_work: 0.3334 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  13065  Z= 0.129
  Angle     :  0.507   5.425  17780  Z= 0.265
  Chirality :  0.045   0.143   1955
  Planarity :  0.004   0.042   2265
  Dihedral  :  4.319  18.404   1715
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  9.46 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.22), residues: 1540
  helix:  1.17 (0.23), residues: 530
  sheet:  1.60 (0.26), residues: 440
  loop : -2.06 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 206 
 HIS   0.003   0.001   HIS A 177 
 PHE   0.009   0.001   PHE D 116 
 TYR   0.007   0.001   TYR D 148 
 ARG   0.003   0.000   ARG D 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03196 (  600)
  hydrogen bonds       : angle       4.43297 ( 1995)
  covalent geometry    : bond        0.00302 (13065)
  covalent geometry    : angle       0.50720 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 1.426 
Fit side-chains
REVERT: A  150 GLU cc_start: 0.7866 (pm20) cc_final: 0.7435 (mp0)
REVERT: A  155 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6888 (mm-30)
REVERT: A  156 GLU cc_start: 0.7803 (tt0) cc_final: 0.7378 (tt0)
REVERT: A  187 GLU cc_start: 0.7566 (tt0) cc_final: 0.7332 (mt-10)
REVERT: B   27 ASN cc_start: 0.7945 (t0) cc_final: 0.7660 (t0)
REVERT: B   69 ASN cc_start: 0.7462 (m-40) cc_final: 0.7180 (m-40)
REVERT: B   90 LYS cc_start: 0.8355 (pttt) cc_final: 0.7855 (ptpp)
REVERT: B   93 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8196 (mtp)
REVERT: B  150 GLU cc_start: 0.7806 (pm20) cc_final: 0.7248 (mp0)
REVERT: B  155 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6653 (mm-30)
REVERT: B  156 GLU cc_start: 0.7724 (tt0) cc_final: 0.7342 (tt0)
REVERT: B  174 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7507 (ttm-80)
REVERT: C   27 ASN cc_start: 0.8261 (t0) cc_final: 0.8056 (t0)
REVERT: C   29 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7713 (tt)
REVERT: C   34 LYS cc_start: 0.8412 (mttm) cc_final: 0.8073 (mttm)
REVERT: C   90 LYS cc_start: 0.8199 (pttt) cc_final: 0.7657 (ptpp)
REVERT: C   93 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8275 (mtp)
REVERT: C  150 GLU cc_start: 0.7654 (pm20) cc_final: 0.7297 (mp0)
REVERT: C  155 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6781 (mm-30)
REVERT: D   27 ASN cc_start: 0.8048 (t0) cc_final: 0.7440 (t0)
REVERT: D   90 LYS cc_start: 0.8341 (pttt) cc_final: 0.7751 (ptpp)
REVERT: D   93 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8318 (mtp)
REVERT: D  137 ASN cc_start: 0.7654 (p0) cc_final: 0.7333 (p0)
REVERT: D  150 GLU cc_start: 0.7709 (pm20) cc_final: 0.7227 (mp0)
REVERT: D  155 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6870 (mm-30)
REVERT: D  159 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6867 (pt0)
REVERT: D  163 ARG cc_start: 0.7397 (mmt90) cc_final: 0.6997 (mmt90)
REVERT: D  174 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7778 (ttm-80)
REVERT: D  176 ASP cc_start: 0.8012 (m-30) cc_final: 0.7686 (m-30)
REVERT: E   34 LYS cc_start: 0.8326 (mttm) cc_final: 0.8091 (mmtp)
REVERT: E   93 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8332 (mtp)
REVERT: E  155 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6725 (mm-30)
REVERT: E  185 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7283 (pt0)
REVERT: E  239 MET cc_start: 0.7566 (ttp) cc_final: 0.7352 (ttp)
  outliers start: 15
  outliers final: 6
  residues processed: 167
  average time/residue: 1.5511
  time to fit residues: 278.5773
Evaluate side-chains
  169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  159 GLU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 152 optimal weight:    7.9990
   chunk 81 optimal weight:    0.6980
   chunk 125 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 153 optimal weight:    0.8980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
B 233 GLN
E  27 ASN
E 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.153310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.119863 restraints weight = 14403.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.11
r_work: 0.3328 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  13065  Z= 0.143
  Angle     :  0.516   5.515  17780  Z= 0.270
  Chirality :  0.045   0.136   1955
  Planarity :  0.004   0.042   2265
  Dihedral  :  4.286  18.541   1715
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.19 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.22), residues: 1540
  helix:  1.31 (0.23), residues: 530
  sheet:  1.66 (0.27), residues: 435
  loop : -2.02 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 206 
 HIS   0.004   0.001   HIS A 177 
 PHE   0.011   0.001   PHE D 116 
 TYR   0.007   0.001   TYR D 148 
 ARG   0.004   0.001   ARG C 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (  600)
  hydrogen bonds       : angle       4.36898 ( 1995)
  covalent geometry    : bond        0.00338 (13065)
  covalent geometry    : angle       0.51602 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 1.287 
Fit side-chains
REVERT: A   36 ASP cc_start: 0.8915 (t0) cc_final: 0.8451 (t70)
REVERT: A   69 ASN cc_start: 0.7582 (m-40) cc_final: 0.7368 (m-40)
REVERT: A  150 GLU cc_start: 0.7862 (pm20) cc_final: 0.7466 (mp0)
REVERT: A  155 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6868 (mm-30)
REVERT: A  156 GLU cc_start: 0.7814 (tt0) cc_final: 0.7412 (tt0)
REVERT: B   27 ASN cc_start: 0.8121 (t0) cc_final: 0.7694 (t0)
REVERT: B   36 ASP cc_start: 0.8969 (t0) cc_final: 0.8752 (t70)
REVERT: B   69 ASN cc_start: 0.7552 (m-40) cc_final: 0.7283 (m-40)
REVERT: B   90 LYS cc_start: 0.8429 (pttt) cc_final: 0.7940 (ptpp)
REVERT: B   93 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8228 (mtp)
REVERT: B  155 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6820 (mm-30)
REVERT: B  156 GLU cc_start: 0.7794 (tt0) cc_final: 0.7376 (tt0)
REVERT: B  163 ARG cc_start: 0.7425 (mmt90) cc_final: 0.7166 (mmp80)
REVERT: C   29 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7788 (tt)
REVERT: C   36 ASP cc_start: 0.8907 (t0) cc_final: 0.8590 (t70)
REVERT: C   90 LYS cc_start: 0.8265 (pttt) cc_final: 0.7722 (ptpp)
REVERT: C  150 GLU cc_start: 0.7779 (pm20) cc_final: 0.7364 (mp0)
REVERT: C  155 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6836 (mm-30)
REVERT: C  159 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6790 (pt0)
REVERT: D   90 LYS cc_start: 0.8388 (pttt) cc_final: 0.7828 (ptpp)
REVERT: D   93 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8310 (mtp)
REVERT: D  137 ASN cc_start: 0.7669 (p0) cc_final: 0.7351 (p0)
REVERT: D  150 GLU cc_start: 0.7836 (pm20) cc_final: 0.7360 (mp0)
REVERT: D  155 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6907 (mm-30)
REVERT: D  163 ARG cc_start: 0.7361 (mmt90) cc_final: 0.7150 (mmp80)
REVERT: D  176 ASP cc_start: 0.7991 (m-30) cc_final: 0.7656 (m-30)
REVERT: D  187 GLU cc_start: 0.7533 (tt0) cc_final: 0.7265 (mt-10)
REVERT: E   36 ASP cc_start: 0.8800 (t0) cc_final: 0.8567 (t70)
REVERT: E   93 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8366 (mtp)
REVERT: E  150 GLU cc_start: 0.7912 (pm20) cc_final: 0.7429 (mp0)
REVERT: E  155 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6980 (mm-30)
REVERT: E  156 GLU cc_start: 0.7762 (tt0) cc_final: 0.7372 (tt0)
REVERT: E  185 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7371 (pt0)
  outliers start: 24
  outliers final: 12
  residues processed: 169
  average time/residue: 1.5153
  time to fit residues: 274.9799
Evaluate side-chains
  171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  159 GLU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  221 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0770
   chunk 63 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 99 optimal weight:    0.3980
   chunk 120 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
E  27 ASN
E 233 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.151578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.118713 restraints weight = 14353.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.16
r_work: 0.3338 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  13065  Z= 0.112
  Angle     :  0.483   5.304  17780  Z= 0.252
  Chirality :  0.044   0.140   1955
  Planarity :  0.004   0.041   2265
  Dihedral  :  4.092  17.966   1715
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.27 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.22), residues: 1540
  helix:  1.44 (0.23), residues: 530
  sheet:  1.76 (0.27), residues: 435
  loop : -1.99 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 206 
 HIS   0.003   0.001   HIS A 177 
 PHE   0.009   0.001   PHE D 116 
 TYR   0.006   0.001   TYR D 148 
 ARG   0.004   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02838 (  600)
  hydrogen bonds       : angle       4.20963 ( 1995)
  covalent geometry    : bond        0.00257 (13065)
  covalent geometry    : angle       0.48307 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 1.417 
Fit side-chains
REVERT: A   36 ASP cc_start: 0.8833 (t0) cc_final: 0.8627 (t0)
REVERT: A  150 GLU cc_start: 0.7799 (pm20) cc_final: 0.7445 (mp0)
REVERT: A  155 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6849 (mm-30)
REVERT: A  156 GLU cc_start: 0.7826 (tt0) cc_final: 0.7410 (tt0)
REVERT: B   27 ASN cc_start: 0.7913 (t0) cc_final: 0.7571 (t0)
REVERT: B   69 ASN cc_start: 0.7436 (m-40) cc_final: 0.7194 (m-40)
REVERT: B   90 LYS cc_start: 0.8338 (pttt) cc_final: 0.7839 (ptpp)
REVERT: B   93 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8182 (mtp)
REVERT: B  137 ASN cc_start: 0.7426 (p0) cc_final: 0.7115 (p0)
REVERT: B  150 GLU cc_start: 0.7771 (pm20) cc_final: 0.7222 (mp0)
REVERT: B  155 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6693 (mm-30)
REVERT: B  156 GLU cc_start: 0.7755 (tt0) cc_final: 0.7311 (tt0)
REVERT: B  163 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7137 (mmp80)
REVERT: B  174 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7513 (ttm-80)
REVERT: C   29 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7690 (tt)
REVERT: C   90 LYS cc_start: 0.8179 (pttt) cc_final: 0.7582 (ptpp)
REVERT: C   93 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8285 (mtp)
REVERT: C  137 ASN cc_start: 0.7417 (p0) cc_final: 0.7149 (p0)
REVERT: C  150 GLU cc_start: 0.7740 (pm20) cc_final: 0.7306 (mp0)
REVERT: C  155 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6808 (mm-30)
REVERT: C  159 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6558 (pt0)
REVERT: D   27 ASN cc_start: 0.8009 (t0) cc_final: 0.7466 (t0)
REVERT: D   90 LYS cc_start: 0.8294 (pttt) cc_final: 0.7791 (ptpp)
REVERT: D   93 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (mtp)
REVERT: D  137 ASN cc_start: 0.7509 (p0) cc_final: 0.7156 (p0)
REVERT: D  150 GLU cc_start: 0.7783 (pm20) cc_final: 0.7292 (mp0)
REVERT: D  155 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6816 (mm-30)
REVERT: D  159 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6828 (pt0)
REVERT: D  163 ARG cc_start: 0.7324 (mmt90) cc_final: 0.6989 (mmp80)
REVERT: D  176 ASP cc_start: 0.7930 (m-30) cc_final: 0.7570 (m-30)
REVERT: D  187 GLU cc_start: 0.7456 (tt0) cc_final: 0.7160 (mt-10)
REVERT: E   93 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8362 (mtp)
REVERT: E  155 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6907 (mm-30)
REVERT: E  185 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7367 (pt0)
  outliers start: 29
  outliers final: 12
  residues processed: 170
  average time/residue: 1.4606
  time to fit residues: 267.4547
Evaluate side-chains
  171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  185 GLN
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  159 GLU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  159 GLU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 133 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 149 optimal weight:    0.9980
   chunk 124 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 118 optimal weight:    4.9990
   chunk 148 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
C  27 ASN
E  27 ASN
E 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.149171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.117007 restraints weight = 14448.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.14
r_work: 0.3322 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  13065  Z= 0.137
  Angle     :  0.504   5.392  17780  Z= 0.264
  Chirality :  0.045   0.134   1955
  Planarity :  0.004   0.041   2265
  Dihedral  :  4.157  18.467   1715
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.78 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.22), residues: 1540
  helix:  1.49 (0.23), residues: 530
  sheet:  1.69 (0.27), residues: 435
  loop : -2.00 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 206 
 HIS   0.004   0.001   HIS B 177 
 PHE   0.010   0.001   PHE D 116 
 TYR   0.007   0.001   TYR D 148 
 ARG   0.004   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03007 (  600)
  hydrogen bonds       : angle       4.26757 ( 1995)
  covalent geometry    : bond        0.00326 (13065)
  covalent geometry    : angle       0.50411 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 152
  time to evaluate  : 1.292 
Fit side-chains
REVERT: A   36 ASP cc_start: 0.8780 (t0) cc_final: 0.8571 (t0)
REVERT: A   69 ASN cc_start: 0.7480 (m-40) cc_final: 0.7266 (m-40)
REVERT: A  150 GLU cc_start: 0.7821 (pm20) cc_final: 0.7445 (mp0)
REVERT: A  155 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6864 (mm-30)
REVERT: A  156 GLU cc_start: 0.7788 (tt0) cc_final: 0.7391 (tt0)
REVERT: B   27 ASN cc_start: 0.7989 (t0) cc_final: 0.7486 (t0)
REVERT: B   36 ASP cc_start: 0.8952 (t0) cc_final: 0.8727 (t70)
REVERT: B   69 ASN cc_start: 0.7399 (m-40) cc_final: 0.7126 (m-40)
REVERT: B   90 LYS cc_start: 0.8345 (pttt) cc_final: 0.7837 (ptpp)
REVERT: B   93 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8161 (mtp)
REVERT: B  155 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6675 (mm-30)
REVERT: B  156 GLU cc_start: 0.7814 (tt0) cc_final: 0.7400 (tt0)
REVERT: B  163 ARG cc_start: 0.7409 (mmt90) cc_final: 0.7112 (mmp80)
REVERT: B  174 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7527 (ttm-80)
REVERT: C   34 LYS cc_start: 0.8353 (mttm) cc_final: 0.7927 (mttm)
REVERT: C   36 ASP cc_start: 0.8906 (t0) cc_final: 0.8606 (t70)
REVERT: C   90 LYS cc_start: 0.8154 (pttt) cc_final: 0.7579 (ptpp)
REVERT: C   93 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (mtp)
REVERT: C  137 ASN cc_start: 0.7478 (p0) cc_final: 0.7169 (p0)
REVERT: C  150 GLU cc_start: 0.7760 (pm20) cc_final: 0.7293 (mp0)
REVERT: C  155 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6736 (mm-30)
REVERT: C  159 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6857 (pt0)
REVERT: D   69 ASN cc_start: 0.7408 (m-40) cc_final: 0.7167 (m-40)
REVERT: D   86 ASP cc_start: 0.7658 (t70) cc_final: 0.7393 (t0)
REVERT: D   90 LYS cc_start: 0.8258 (pttt) cc_final: 0.7745 (ptpp)
REVERT: D   93 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8259 (mtp)
REVERT: D  137 ASN cc_start: 0.7567 (p0) cc_final: 0.7189 (p0)
REVERT: D  150 GLU cc_start: 0.7813 (pm20) cc_final: 0.7221 (mt-10)
REVERT: D  155 GLU cc_start: 0.7653 (mt-10) cc_final: 0.6837 (mm-30)
REVERT: D  159 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6972 (pt0)
REVERT: D  163 ARG cc_start: 0.7336 (mmt90) cc_final: 0.7132 (mmp80)
REVERT: D  176 ASP cc_start: 0.7929 (m-30) cc_final: 0.7582 (m-30)
REVERT: D  187 GLU cc_start: 0.7449 (tt0) cc_final: 0.7166 (mt-10)
REVERT: E   36 ASP cc_start: 0.8859 (t0) cc_final: 0.8602 (t70)
REVERT: E   93 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8335 (mtp)
REVERT: E  155 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6925 (mm-30)
REVERT: E  185 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7375 (pt0)
  outliers start: 33
  outliers final: 22
  residues processed: 170
  average time/residue: 1.4847
  time to fit residues: 271.3150
Evaluate side-chains
  174 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  159 GLU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  159 GLU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  195 ILE
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 144 optimal weight:    1.9990
   chunk 140 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 151 optimal weight:   10.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.145031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112199 restraints weight = 14542.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.15
r_work: 0.3259 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034  13065  Z= 0.256
  Angle     :  0.610   7.632  17780  Z= 0.323
  Chirality :  0.049   0.148   1955
  Planarity :  0.004   0.041   2265
  Dihedral  :  4.694  22.116   1715
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.72 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.22), residues: 1540
  helix:  1.29 (0.23), residues: 530
  sheet:  1.45 (0.28), residues: 435
  loop : -2.13 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 206 
 HIS   0.007   0.002   HIS B 177 
 PHE   0.013   0.002   PHE E 116 
 TYR   0.010   0.002   TYR E 148 
 ARG   0.005   0.001   ARG E  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  600)
  hydrogen bonds       : angle       4.64285 ( 1995)
  covalent geometry    : bond        0.00627 (13065)
  covalent geometry    : angle       0.60961 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 145
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A   36 ASP cc_start: 0.8902 (t0) cc_final: 0.8609 (t70)
REVERT: A   69 ASN cc_start: 0.7710 (m-40) cc_final: 0.7489 (m-40)
REVERT: A   99 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6446 (ptm160)
REVERT: A  155 GLU cc_start: 0.7643 (mt-10) cc_final: 0.6961 (mm-30)
REVERT: A  156 GLU cc_start: 0.7687 (tt0) cc_final: 0.7269 (tt0)
REVERT: B   27 ASN cc_start: 0.8306 (t0) cc_final: 0.7842 (t0)
REVERT: B   29 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7873 (tt)
REVERT: B   36 ASP cc_start: 0.8967 (t0) cc_final: 0.8766 (t70)
REVERT: B   90 LYS cc_start: 0.8428 (pttt) cc_final: 0.7922 (ptpp)
REVERT: B  155 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6895 (mm-30)
REVERT: B  156 GLU cc_start: 0.7694 (tt0) cc_final: 0.7355 (tt0)
REVERT: C   29 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7719 (tt)
REVERT: C   36 ASP cc_start: 0.8945 (t0) cc_final: 0.8695 (t70)
REVERT: C   90 LYS cc_start: 0.8303 (pttt) cc_final: 0.7722 (ptpp)
REVERT: C   99 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7342 (ptm-80)
REVERT: C  155 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6748 (mm-30)
REVERT: D   34 LYS cc_start: 0.8452 (mttm) cc_final: 0.8066 (mmtp)
REVERT: D   69 ASN cc_start: 0.7716 (m-40) cc_final: 0.7458 (m-40)
REVERT: D   86 ASP cc_start: 0.7717 (t70) cc_final: 0.7484 (t0)
REVERT: D   93 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8285 (mtp)
REVERT: D  137 ASN cc_start: 0.7956 (p0) cc_final: 0.7594 (p0)
REVERT: D  150 GLU cc_start: 0.7899 (pm20) cc_final: 0.7306 (mt-10)
REVERT: D  155 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6969 (mm-30)
REVERT: D  176 ASP cc_start: 0.7953 (m-30) cc_final: 0.7650 (m-30)
REVERT: D  187 GLU cc_start: 0.7447 (tt0) cc_final: 0.7183 (mt-10)
REVERT: E   69 ASN cc_start: 0.7678 (m-40) cc_final: 0.7432 (m-40)
REVERT: E  150 GLU cc_start: 0.7943 (pm20) cc_final: 0.7467 (mp0)
REVERT: E  155 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7016 (mm-30)
REVERT: E  156 GLU cc_start: 0.7757 (tt0) cc_final: 0.7448 (tt0)
REVERT: E  185 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7519 (pt0)
  outliers start: 43
  outliers final: 21
  residues processed: 173
  average time/residue: 1.4690
  time to fit residues: 273.2250
Evaluate side-chains
  165 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ARG
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  221 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  221 SER
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  221 SER
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  221 SER
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0670
   chunk 153 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 101 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 28 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0270
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
C  69 ASN
D  27 ASN
E  27 ASN
E 233 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.152134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.119622 restraints weight = 14374.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.16
r_work: 0.3361 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13065  Z= 0.093
  Angle     :  0.470   5.443  17780  Z= 0.245
  Chirality :  0.044   0.141   1955
  Planarity :  0.004   0.044   2265
  Dihedral  :  4.046  18.650   1715
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.73 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.22), residues: 1540
  helix:  1.53 (0.23), residues: 530
  sheet:  1.70 (0.27), residues: 440
  loop : -2.10 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C 206 
 HIS   0.002   0.000   HIS C 177 
 PHE   0.008   0.001   PHE D 116 
 TYR   0.007   0.001   TYR B 203 
 ARG   0.005   0.000   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02580 (  600)
  hydrogen bonds       : angle       4.17940 ( 1995)
  covalent geometry    : bond        0.00204 (13065)
  covalent geometry    : angle       0.47016 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ASN cc_start: 0.7543 (m-40) cc_final: 0.7320 (m-40)
REVERT: A   93 MET cc_start: 0.8479 (mtp) cc_final: 0.8209 (mmm)
REVERT: A  150 GLU cc_start: 0.7852 (pm20) cc_final: 0.7415 (mp0)
REVERT: A  155 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6884 (mm-30)
REVERT: A  156 GLU cc_start: 0.7778 (tt0) cc_final: 0.7394 (tt0)
REVERT: B   27 ASN cc_start: 0.7946 (t0) cc_final: 0.7601 (t0)
REVERT: B   69 ASN cc_start: 0.7515 (m-40) cc_final: 0.7253 (m-40)
REVERT: B   90 LYS cc_start: 0.8385 (pttt) cc_final: 0.7885 (ptpp)
REVERT: B   93 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8242 (mtp)
REVERT: B  155 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6682 (mm-30)
REVERT: B  156 GLU cc_start: 0.7750 (tt0) cc_final: 0.7370 (tt0)
REVERT: B  174 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7550 (ttm-80)
REVERT: C   90 LYS cc_start: 0.8242 (pttt) cc_final: 0.7639 (ptpp)
REVERT: C   93 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8295 (mtp)
REVERT: C  137 ASN cc_start: 0.7466 (p0) cc_final: 0.7255 (p0)
REVERT: C  155 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6752 (mm-30)
REVERT: D   27 ASN cc_start: 0.7987 (t0) cc_final: 0.7306 (t0)
REVERT: D   34 LYS cc_start: 0.8377 (mttm) cc_final: 0.8035 (mmtp)
REVERT: D   69 ASN cc_start: 0.7513 (m-40) cc_final: 0.7280 (m-40)
REVERT: D   86 ASP cc_start: 0.7675 (t70) cc_final: 0.7435 (t70)
REVERT: D   90 LYS cc_start: 0.8360 (pttt) cc_final: 0.7839 (ptpp)
REVERT: D  137 ASN cc_start: 0.7488 (p0) cc_final: 0.7136 (p0)
REVERT: D  150 GLU cc_start: 0.7738 (pm20) cc_final: 0.7157 (mt-10)
REVERT: D  155 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6912 (mm-30)
REVERT: D  163 ARG cc_start: 0.7428 (mmp80) cc_final: 0.7188 (mmp80)
REVERT: D  174 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7787 (ttm-80)
REVERT: D  187 GLU cc_start: 0.7552 (tt0) cc_final: 0.7316 (mt-10)
REVERT: E   34 LYS cc_start: 0.8392 (mttm) cc_final: 0.8175 (mmtp)
REVERT: E   93 MET cc_start: 0.8642 (ttp) cc_final: 0.8411 (mtp)
REVERT: E  150 GLU cc_start: 0.7816 (pm20) cc_final: 0.7292 (mp0)
REVERT: E  155 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6915 (mm-30)
REVERT: E  156 GLU cc_start: 0.7798 (tt0) cc_final: 0.7480 (tt0)
REVERT: E  163 ARG cc_start: 0.7334 (mmt90) cc_final: 0.7119 (mmt90)
REVERT: E  185 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7439 (pt0)
  outliers start: 30
  outliers final: 15
  residues processed: 180
  average time/residue: 1.8014
  time to fit residues: 350.5919
Evaluate side-chains
  167 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 144 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 114 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0970
   chunk 8 optimal weight:    0.0170
   chunk 138 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   chunk 133 optimal weight:    3.9990
   chunk 110 optimal weight:    0.7980
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
B 124 GLN
E  21 ASN
E 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.153236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.120581 restraints weight = 14347.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.16
r_work: 0.3373 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13065  Z= 0.091
  Angle     :  0.468   5.575  17780  Z= 0.243
  Chirality :  0.043   0.132   1955
  Planarity :  0.004   0.047   2265
  Dihedral  :  3.868  19.920   1715
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.67 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.23), residues: 1540
  helix:  1.70 (0.23), residues: 530
  sheet:  1.79 (0.27), residues: 440
  loop : -1.97 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP C 206 
 HIS   0.002   0.000   HIS B 177 
 PHE   0.007   0.001   PHE D 106 
 TYR   0.005   0.001   TYR B 203 
 ARG   0.005   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02536 (  600)
  hydrogen bonds       : angle       4.00957 ( 1995)
  covalent geometry    : bond        0.00202 (13065)
  covalent geometry    : angle       0.46812 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 2.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7408 (pt0)
REVERT: A   36 ASP cc_start: 0.8876 (t0) cc_final: 0.8464 (t70)
REVERT: A   93 MET cc_start: 0.8490 (mtp) cc_final: 0.8211 (mmm)
REVERT: A  150 GLU cc_start: 0.7817 (pm20) cc_final: 0.7436 (mp0)
REVERT: A  155 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6936 (mm-30)
REVERT: A  156 GLU cc_start: 0.7769 (tt0) cc_final: 0.7371 (tt0)
REVERT: A  163 ARG cc_start: 0.7132 (mmt90) cc_final: 0.6908 (mmp80)
REVERT: B   27 ASN cc_start: 0.8083 (t0) cc_final: 0.7657 (t0)
REVERT: B   69 ASN cc_start: 0.7437 (m-40) cc_final: 0.7167 (m-40)
REVERT: B   90 LYS cc_start: 0.8341 (pttt) cc_final: 0.7886 (ptpp)
REVERT: B   93 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8237 (mtp)
REVERT: B  150 GLU cc_start: 0.7819 (pm20) cc_final: 0.7181 (mp0)
REVERT: B  155 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6676 (mm-30)
REVERT: B  156 GLU cc_start: 0.7827 (tt0) cc_final: 0.7468 (tt0)
REVERT: C   36 ASP cc_start: 0.8962 (t0) cc_final: 0.8516 (t70)
REVERT: C   90 LYS cc_start: 0.8230 (pttt) cc_final: 0.7694 (ptpp)
REVERT: C  155 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6777 (mm-30)
REVERT: D   27 ASN cc_start: 0.7827 (t0) cc_final: 0.7399 (t0)
REVERT: D   34 LYS cc_start: 0.8351 (mttm) cc_final: 0.8119 (mmtp)
REVERT: D   90 LYS cc_start: 0.8356 (pttt) cc_final: 0.7812 (ptpp)
REVERT: D  137 ASN cc_start: 0.7517 (p0) cc_final: 0.7168 (p0)
REVERT: D  150 GLU cc_start: 0.7691 (pm20) cc_final: 0.7149 (mt-10)
REVERT: D  155 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6857 (mm-30)
REVERT: D  187 GLU cc_start: 0.7533 (tt0) cc_final: 0.7265 (mt-10)
REVERT: E   34 LYS cc_start: 0.8404 (mttm) cc_final: 0.8187 (mmtp)
REVERT: E   93 MET cc_start: 0.8620 (ttp) cc_final: 0.8383 (mtp)
REVERT: E  150 GLU cc_start: 0.7761 (pm20) cc_final: 0.7287 (mp0)
REVERT: E  155 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6920 (mm-30)
REVERT: E  156 GLU cc_start: 0.7695 (tt0) cc_final: 0.7340 (tt0)
REVERT: E  185 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7448 (pt0)
  outliers start: 24
  outliers final: 13
  residues processed: 170
  average time/residue: 1.6109
  time to fit residues: 297.1537
Evaluate side-chains
  163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 144 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 140 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
A 184 ASN
A 233 GLN
B 124 GLN
D  21 ASN
E 233 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.153637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.120068 restraints weight = 14433.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.14
r_work: 0.3353 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13065  Z= 0.120
  Angle     :  0.495   5.588  17780  Z= 0.258
  Chirality :  0.044   0.133   1955
  Planarity :  0.004   0.045   2265
  Dihedral  :  3.990  19.559   1715
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.96 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.23), residues: 1540
  helix:  1.70 (0.23), residues: 530
  sheet:  1.78 (0.27), residues: 435
  loop : -1.93 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C 206 
 HIS   0.003   0.001   HIS B 177 
 PHE   0.008   0.001   PHE E 116 
 TYR   0.006   0.001   TYR B 203 
 ARG   0.007   0.000   ARG E 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02780 (  600)
  hydrogen bonds       : angle       4.11513 ( 1995)
  covalent geometry    : bond        0.00283 (13065)
  covalent geometry    : angle       0.49546 (17780)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 1.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 ASP cc_start: 0.8864 (t0) cc_final: 0.8434 (t70)
REVERT: A  150 GLU cc_start: 0.7853 (pm20) cc_final: 0.7466 (mp0)
REVERT: A  155 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6909 (mm-30)
REVERT: A  156 GLU cc_start: 0.7783 (tt0) cc_final: 0.7382 (tt0)
REVERT: B   69 ASN cc_start: 0.7463 (m-40) cc_final: 0.7199 (m-40)
REVERT: B   90 LYS cc_start: 0.8349 (pttt) cc_final: 0.7858 (ptpp)
REVERT: B   93 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8256 (mtp)
REVERT: B  145 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7803 (tt)
REVERT: B  155 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6706 (mm-30)
REVERT: B  156 GLU cc_start: 0.7806 (tt0) cc_final: 0.7436 (tt0)
REVERT: B  174 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7569 (ttm-80)
REVERT: C   36 ASP cc_start: 0.8956 (t0) cc_final: 0.8528 (t70)
REVERT: C   90 LYS cc_start: 0.8207 (pttt) cc_final: 0.7649 (ptpp)
REVERT: C  155 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6797 (mm-30)
REVERT: D   86 ASP cc_start: 0.7779 (t70) cc_final: 0.7524 (t0)
REVERT: D   90 LYS cc_start: 0.8409 (pttt) cc_final: 0.7901 (ptpp)
REVERT: D  137 ASN cc_start: 0.7597 (p0) cc_final: 0.7242 (p0)
REVERT: D  150 GLU cc_start: 0.7768 (pm20) cc_final: 0.7201 (mt-10)
REVERT: D  155 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6917 (mm-30)
REVERT: D  174 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7708 (ttm-80)
REVERT: D  187 GLU cc_start: 0.7467 (tt0) cc_final: 0.7237 (mt-10)
REVERT: E   93 MET cc_start: 0.8609 (ttp) cc_final: 0.8383 (mtp)
REVERT: E  155 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6912 (mm-30)
REVERT: E  185 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7426 (pt0)
  outliers start: 19
  outliers final: 14
  residues processed: 158
  average time/residue: 1.4467
  time to fit residues: 246.8359
Evaluate side-chains
  159 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   93 MET
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain E residue  185 GLN
Chi-restraints excluded: chain E residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 139 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 119 optimal weight:    0.8980
   chunk 114 optimal weight:    0.5980
   chunk 86 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0970
   chunk 134 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 233 GLN
B 124 GLN
E 233 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.152455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.119803 restraints weight = 14292.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.16
r_work: 0.3355 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13065  Z= 0.098
  Angle     :  0.476   5.728  17780  Z= 0.247
  Chirality :  0.044   0.133   1955
  Planarity :  0.004   0.045   2265
  Dihedral  :  3.886  19.290   1715
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.88 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.23), residues: 1540
  helix:  1.73 (0.23), residues: 530
  sheet:  1.76 (0.27), residues: 440
  loop : -1.91 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP C 206 
 HIS   0.002   0.000   HIS B 177 
 PHE   0.008   0.001   PHE D 106 
 TYR   0.006   0.001   TYR B 203 
 ARG   0.007   0.000   ARG D 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02567 (  600)
  hydrogen bonds       : angle       4.02131 ( 1995)
  covalent geometry    : bond        0.00223 (13065)
  covalent geometry    : angle       0.47642 (17780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8728.67 seconds
wall clock time: 151 minutes 49.82 seconds (9109.82 seconds total)