Starting phenix.real_space_refine
on Mon Jul 28 13:14:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ehg_28147/07_2025/8ehg_28147.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ehg_28147/07_2025/8ehg_28147.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ehg_28147/07_2025/8ehg_28147.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ehg_28147/07_2025/8ehg_28147.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ehg_28147/07_2025/8ehg_28147.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ehg_28147/07_2025/8ehg_28147.cif"
  }
  resolution = 2.24
  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=   0.001 sd=   0.112
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 7.64, per 1000 atoms: 0.73
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (103.627, 94.043, 79.667, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1980      8.00
     N    1860      7.00
     C    6588      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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      54.8% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 45
      removed outlier: 4.326A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ARG A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.864A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 226
    Processing helix  chain 'A' and resid 244 through 258
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 6.625A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 338
      removed outlier: 3.606A  pdb=" N   ARG A 330 " --> pdb=" O   GLU A 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 45
      removed outlier: 4.326A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ARG B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.864A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 226
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 6.625A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 338
      removed outlier: 3.606A  pdb=" N   ARG B 330 " --> pdb=" O   GLU B 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 45
      removed outlier: 4.326A  pdb=" N   LYS C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ARG C  42 " --> pdb=" O   SER C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 79 through 84
      removed outlier: 3.864A  pdb=" N   TYR C  84 " --> pdb=" O   HIS C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 226
    Processing helix  chain 'C' and resid 244 through 258
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 6.625A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 338
      removed outlier: 3.606A  pdb=" N   ARG C 330 " --> pdb=" O   GLU C 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 35 through 45
      removed outlier: 4.326A  pdb=" N   LYS D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ARG D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 79 through 84
      removed outlier: 3.864A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 100
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 226
    Processing helix  chain 'D' and resid 244 through 258
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 6.625A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 338
      removed outlier: 3.606A  pdb=" N   ARG D 330 " --> pdb=" O   GLU D 326 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.756A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   GLY A  74 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   GLY A 105 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   LEU A  78 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A 104 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE A 106 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32
      removed outlier: 6.756A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   GLY B  74 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   GLY B 105 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   LEU B  78 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   LYS B 146 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE B 106 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   GLU B 187 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLU B 189 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   CYS B 149 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU B 191 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32
      removed outlier: 6.756A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ALA C  32 " --> pdb=" O   LEU C  78 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   GLY C  74 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   GLY C 105 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   LEU C  78 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL C 104 " --> pdb=" O   PHE C 144 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   LYS C 146 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE C 106 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ARG C 148 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ALA C 145 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   GLU C 187 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   TRP C 147 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLU C 189 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   CYS C 149 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU C 191 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LEU C 151 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.756A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   GLY D  74 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   GLY D 105 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LYS D 107 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   LEU D  78 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL D 104 " --> pdb=" O   PHE D 144 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   LYS D 146 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE D 106 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ARG D 148 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ALA D 145 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   GLU D 187 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   TRP D 147 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLU D 189 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   CYS D 149 " --> pdb=" O   GLU D 189 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU D 191 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LEU D 151 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    544 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.67

  Time building geometry restraints manager: 2.87 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3520
        1.34 -     1.46: 1956
        1.46 -     1.58: 5140
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   GLY C 302 "
       pdb=" O   GLY C 302 "
    ideal  model  delta    sigma   weight residual
    1.245  1.234  0.011 1.19e-02 7.06e+03 8.33e-01
  bond pdb=" C   GLY B 302 "
       pdb=" O   GLY B 302 "
    ideal  model  delta    sigma   weight residual
    1.245  1.234  0.011 1.19e-02 7.06e+03 8.33e-01
  bond pdb=" C   GLY D 302 "
       pdb=" O   GLY D 302 "
    ideal  model  delta    sigma   weight residual
    1.245  1.234  0.011 1.19e-02 7.06e+03 8.33e-01
  bond pdb=" C   GLY A 302 "
       pdb=" O   GLY A 302 "
    ideal  model  delta    sigma   weight residual
    1.245  1.234  0.011 1.19e-02 7.06e+03 8.33e-01
  bond pdb=" C   VAL C  23 "
       pdb=" O   VAL C  23 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.19e-02 7.06e+03 7.46e-01
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 14128
        1.41 -     2.83: 284
        2.83 -     4.24: 40
        4.24 -     5.65: 4
        5.65 -     7.07: 8
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" O   GLY C 302 "
        pdb=" C   GLY C 302 "
        pdb=" N   ARG C 303 "
      ideal   model   delta    sigma   weight residual
     121.85  123.29   -1.44 5.60e-01 3.19e+00 6.65e+00
  angle pdb=" O   GLY D 302 "
        pdb=" C   GLY D 302 "
        pdb=" N   ARG D 303 "
      ideal   model   delta    sigma   weight residual
     121.85  123.29   -1.44 5.60e-01 3.19e+00 6.65e+00
  angle pdb=" O   GLY A 302 "
        pdb=" C   GLY A 302 "
        pdb=" N   ARG A 303 "
      ideal   model   delta    sigma   weight residual
     121.85  123.29   -1.44 5.60e-01 3.19e+00 6.65e+00
  angle pdb=" O   GLY B 302 "
        pdb=" C   GLY B 302 "
        pdb=" N   ARG B 303 "
      ideal   model   delta    sigma   weight residual
     121.85  123.29   -1.44 5.60e-01 3.19e+00 6.65e+00
  angle pdb=" CA  TYR B 213 "
        pdb=" CB  TYR B 213 "
        pdb=" CG  TYR B 213 "
      ideal   model   delta    sigma   weight residual
     113.90  110.16    3.74 1.80e+00 3.09e-01 4.33e+00
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 5852
       17.24 -    34.48: 412
       34.48 -    51.72: 160
       51.72 -    68.96: 60
       68.96 -    86.20: 20
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  THR D 122 "
           pdb=" C   THR D 122 "
           pdb=" N   THR D 123 "
           pdb=" CA  THR D 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.53   18.47     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  THR A 122 "
           pdb=" C   THR A 122 "
           pdb=" N   THR A 123 "
           pdb=" CA  THR A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.53   18.47     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  THR C 122 "
           pdb=" C   THR C 122 "
           pdb=" N   THR C 123 "
           pdb=" CA  THR C 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.53   18.47     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1014
       0.027 -    0.054: 358
       0.054 -    0.081: 160
       0.081 -    0.108: 96
       0.108 -    0.136: 16
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  VAL C 186 "
            pdb=" N   VAL C 186 "
            pdb=" C   VAL C 186 "
            pdb=" CB  VAL C 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  VAL A 186 "
            pdb=" N   VAL A 186 "
            pdb=" C   VAL A 186 "
            pdb=" CB  VAL A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  VAL D 186 "
            pdb=" N   VAL D 186 "
            pdb=" C   VAL D 186 "
            pdb=" CB  VAL D 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 144 "   -0.010 2.00e-02 2.50e+03   7.96e-03 1.11e+00
        pdb=" CG  PHE C 144 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 144 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 144 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 144 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 144 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 144 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 144 "   -0.010 2.00e-02 2.50e+03   7.96e-03 1.11e+00
        pdb=" CG  PHE A 144 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 144 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 144 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 144 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 144 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 144 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 144 "    0.010 2.00e-02 2.50e+03   7.96e-03 1.11e+00
        pdb=" CG  PHE B 144 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 144 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 144 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 144 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 144 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 144 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2868
        2.81 -     3.33: 10508
        3.33 -     3.86: 19924
        3.86 -     4.38: 22936
        4.38 -     4.90: 37662
  Nonbonded interactions: 93898
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  84 "
            pdb=" OD2 ASP A 140 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OH  TYR B  84 "
            pdb=" OD2 ASP B 140 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OH  TYR D  84 "
            pdb=" OD2 ASP D 140 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OH  TYR C  84 "
            pdb=" OD2 ASP C 140 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OE1 GLU B 277 "
            pdb=" OH  TYR B 342 "
     model   vdw
     2.345 3.040
  ... (remaining 93893 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.520
  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:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     28.580
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:14.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
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      :  0.003   0.022  10672  Z= 0.129
  Angle     :  0.531   7.067  14464  Z= 0.297
  Chirality :  0.039   0.136   1644
  Planarity :  0.004   0.025   1880
  Dihedral  : 16.087  86.201   3984
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.07 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.23), residues: 1364
  helix:  1.56 (0.19), residues: 708
  sheet: -1.06 (0.35), residues: 176
  loop :  0.44 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 147 
 HIS   0.003   0.001   HIS C 237 
 PHE   0.018   0.002   PHE C 144 
 TYR   0.016   0.002   TYR C 213 
 ARG   0.001   0.000   ARG B 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13745 (  544)
  hydrogen bonds       : angle       5.23995 ( 1572)
  covalent geometry    : bond        0.00253 (10672)
  covalent geometry    : angle       0.53070 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.305 
Fit side-chains
  outliers start: 16
  outliers final: 8
  residues processed: 112
  average time/residue: 1.4934
  time to fit residues: 178.6313
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    0.5980
   chunk 103 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 69 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.178118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.160221 restraints weight = 8634.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 0.72
r_work: 0.3735 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 2.21 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.0669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10672  Z= 0.149
  Angle     :  0.544   6.015  14464  Z= 0.286
  Chirality :  0.042   0.128   1644
  Planarity :  0.004   0.024   1880
  Dihedral  :  5.759  56.033   1484
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  8.27 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.22), residues: 1364
  helix:  2.06 (0.19), residues: 712
  sheet: -1.53 (0.38), residues: 144
  loop :  0.51 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 147 
 HIS   0.003   0.001   HIS B  80 
 PHE   0.016   0.002   PHE A 144 
 TYR   0.022   0.002   TYR D 213 
 ARG   0.002   0.000   ARG B 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05049 (  544)
  hydrogen bonds       : angle       3.93335 ( 1572)
  covalent geometry    : bond        0.00327 (10672)
  covalent geometry    : angle       0.54408 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 2.455 
Fit side-chains
REVERT: A   34 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6193 (pm20)
REVERT: B   34 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6191 (pm20)
REVERT: C   34 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6192 (pm20)
REVERT: D   34 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6199 (pm20)
  outliers start: 28
  outliers final: 16
  residues processed: 112
  average time/residue: 1.8635
  time to fit residues: 222.3759
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   49 GLU
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   34 GLU
Chi-restraints excluded: chain B residue   49 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   34 GLU
Chi-restraints excluded: chain C residue   49 GLU
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   34 GLU
Chi-restraints excluded: chain D residue   49 GLU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0570
   chunk 3 optimal weight:    0.0570
   chunk 37 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.3016

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

Flipped N/Q/H residues before XYZ refinement:
A  20 HIS
A  95 GLN
B  20 HIS
B  95 GLN
C  20 HIS
C  95 GLN
D  20 HIS
D  95 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.182254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.164802 restraints weight = 8742.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 0.72
r_work: 0.3800 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 2.19 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.0814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10672  Z= 0.102
  Angle     :  0.465   5.791  14464  Z= 0.242
  Chirality :  0.039   0.121   1644
  Planarity :  0.003   0.024   1880
  Dihedral  :  5.446  55.939   1484
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  8.99 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.23), residues: 1364
  helix:  2.44 (0.19), residues: 720
  sheet: -1.76 (0.37), residues: 164
  loop :  0.63 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 147 
 HIS   0.002   0.001   HIS B  80 
 PHE   0.013   0.001   PHE B 144 
 TYR   0.014   0.001   TYR B 213 
 ARG   0.001   0.000   ARG B 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03974 (  544)
  hydrogen bonds       : angle       3.68856 ( 1572)
  covalent geometry    : bond        0.00219 (10672)
  covalent geometry    : angle       0.46515 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 1.301 
Fit side-chains
  outliers start: 36
  outliers final: 12
  residues processed: 128
  average time/residue: 1.8583
  time to fit residues: 252.1756
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 106 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0980
   chunk 125 optimal weight:    0.6980
   chunk 131 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 109 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.180496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.163298 restraints weight = 8683.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 0.70
r_work: 0.3765 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 2.16 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10672  Z= 0.128
  Angle     :  0.504   5.115  14464  Z= 0.263
  Chirality :  0.041   0.122   1644
  Planarity :  0.004   0.024   1880
  Dihedral  :  5.634  55.911   1484
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.71 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.23), residues: 1364
  helix:  2.40 (0.19), residues: 720
  sheet: -1.68 (0.37), residues: 164
  loop :  0.57 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 147 
 HIS   0.002   0.001   HIS C   4 
 PHE   0.015   0.002   PHE B 144 
 TYR   0.021   0.002   TYR D 213 
 ARG   0.002   0.000   ARG D 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04465 (  544)
  hydrogen bonds       : angle       3.71620 ( 1572)
  covalent geometry    : bond        0.00283 (10672)
  covalent geometry    : angle       0.50432 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 1.550 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5420 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.5426 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5422 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5425 (mpt-90)
  outliers start: 28
  outliers final: 12
  residues processed: 132
  average time/residue: 1.9913
  time to fit residues: 278.3184
Evaluate side-chains
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 115 optimal weight:    0.3980
   chunk 114 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0670
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.181577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.164531 restraints weight = 8686.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 0.69
r_work: 0.3777 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10672  Z= 0.115
  Angle     :  0.484   5.025  14464  Z= 0.253
  Chirality :  0.040   0.120   1644
  Planarity :  0.004   0.025   1880
  Dihedral  :  5.533  55.568   1484
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  :  8.99 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.23), residues: 1364
  helix:  2.44 (0.19), residues: 720
  sheet: -1.71 (0.38), residues: 164
  loop :  0.60 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 147 
 HIS   0.002   0.001   HIS B   2 
 PHE   0.015   0.002   PHE C 144 
 TYR   0.018   0.002   TYR A 213 
 ARG   0.001   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  544)
  hydrogen bonds       : angle       3.64546 ( 1572)
  covalent geometry    : bond        0.00254 (10672)
  covalent geometry    : angle       0.48403 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 96
  time to evaluate  : 1.379 
Fit side-chains
REVERT: A   34 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6188 (pm20)
REVERT: A   42 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5395 (mpt-90)
REVERT: B   34 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6186 (pm20)
REVERT: B   42 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5394 (mpt-90)
REVERT: C   34 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6184 (pm20)
REVERT: C   42 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5396 (mpt-90)
REVERT: D   34 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6185 (pm20)
REVERT: D   42 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5393 (mpt-90)
  outliers start: 44
  outliers final: 20
  residues processed: 128
  average time/residue: 1.9469
  time to fit residues: 263.3251
Evaluate side-chains
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   34 GLU
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   34 GLU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    3 SER
Chi-restraints excluded: chain D residue   34 GLU
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 125 optimal weight:    0.5980
   chunk 132 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.179567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.162291 restraints weight = 8722.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 0.70
r_work: 0.3730 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 2.16 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.139
  Angle     :  0.521   5.473  14464  Z= 0.273
  Chirality :  0.041   0.124   1644
  Planarity :  0.004   0.025   1880
  Dihedral  :  5.715  55.402   1484
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.07 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.23), residues: 1364
  helix:  2.43 (0.19), residues: 712
  sheet: -1.75 (0.37), residues: 164
  loop :  0.60 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 147 
 HIS   0.002   0.001   HIS C   4 
 PHE   0.016   0.002   PHE C 144 
 TYR   0.022   0.002   TYR C 213 
 ARG   0.002   0.000   ARG C 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04627 (  544)
  hydrogen bonds       : angle       3.72999 ( 1572)
  covalent geometry    : bond        0.00308 (10672)
  covalent geometry    : angle       0.52104 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.248 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.5431 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.5428 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.5431 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.5437 (mpt-90)
  outliers start: 32
  outliers final: 20
  residues processed: 136
  average time/residue: 1.5983
  time to fit residues: 230.9057
Evaluate side-chains
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    3 SER
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 60 optimal weight:    0.0980
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0570
   chunk 130 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 119 ASN
B  95 GLN
B 119 ASN
C  95 GLN
C 119 ASN
D  95 GLN
D 119 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.181507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.164369 restraints weight = 8822.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 0.71
r_work: 0.3775 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 2.17 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10672  Z= 0.114
  Angle     :  0.488   5.929  14464  Z= 0.255
  Chirality :  0.040   0.119   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.559  55.297   1484
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.79 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.23), residues: 1364
  helix:  2.49 (0.19), residues: 720
  sheet: -1.73 (0.38), residues: 164
  loop :  0.55 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 147 
 HIS   0.002   0.001   HIS D   4 
 PHE   0.015   0.002   PHE D 144 
 TYR   0.018   0.002   TYR B 213 
 ARG   0.002   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04169 (  544)
  hydrogen bonds       : angle       3.63289 ( 1572)
  covalent geometry    : bond        0.00252 (10672)
  covalent geometry    : angle       0.48833 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 96
  time to evaluate  : 1.165 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5510 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5512 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5510 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5504 (mpt-90)
  outliers start: 32
  outliers final: 20
  residues processed: 124
  average time/residue: 1.7344
  time to fit residues: 227.3391
Evaluate side-chains
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    3 SER
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 121 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.179541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.162318 restraints weight = 8710.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 0.71
r_work: 0.3750 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 2.19 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.139
  Angle     :  0.526   6.141  14464  Z= 0.275
  Chirality :  0.041   0.124   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.711  55.156   1484
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 10.07 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.23), residues: 1364
  helix:  2.42 (0.19), residues: 712
  sheet: -1.77 (0.38), residues: 164
  loop :  0.58 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 147 
 HIS   0.003   0.001   HIS A   2 
 PHE   0.017   0.002   PHE C 144 
 TYR   0.022   0.002   TYR C 213 
 ARG   0.002   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  544)
  hydrogen bonds       : angle       3.71768 ( 1572)
  covalent geometry    : bond        0.00308 (10672)
  covalent geometry    : angle       0.52604 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 112
  time to evaluate  : 1.174 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5522 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.5516 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5520 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5519 (mpt-90)
  outliers start: 36
  outliers final: 20
  residues processed: 140
  average time/residue: 1.6903
  time to fit residues: 250.2121
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    3 SER
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 132 optimal weight:    3.9990
   chunk 123 optimal weight:    0.2980
   chunk 39 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.180178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.162858 restraints weight = 8796.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 0.71
r_work: 0.3758 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 2.20 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10672  Z= 0.132
  Angle     :  0.521   7.529  14464  Z= 0.270
  Chirality :  0.041   0.123   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.675  55.000   1484
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.43 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.23), residues: 1364
  helix:  2.34 (0.19), residues: 720
  sheet: -1.79 (0.37), residues: 164
  loop :  0.54 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 147 
 HIS   0.002   0.001   HIS B   4 
 PHE   0.016   0.002   PHE D 144 
 TYR   0.021   0.002   TYR C 213 
 ARG   0.002   0.000   ARG C 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 (  544)
  hydrogen bonds       : angle       3.70443 ( 1572)
  covalent geometry    : bond        0.00292 (10672)
  covalent geometry    : angle       0.52072 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 1.248 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5501 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5489 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5490 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5499 (mpt-90)
  outliers start: 32
  outliers final: 20
  residues processed: 132
  average time/residue: 1.6404
  time to fit residues: 229.8039
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    3 SER
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 106 optimal weight:    0.0370
   chunk 108 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    0.3980
   chunk 112 optimal weight:    0.8980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.178378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.161366 restraints weight = 8776.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 0.71
r_work: 0.3762 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 2.16 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10672  Z= 0.122
  Angle     :  0.512   7.283  14464  Z= 0.267
  Chirality :  0.040   0.120   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.594  54.908   1484
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 10.43 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.23), residues: 1364
  helix:  2.39 (0.19), residues: 720
  sheet: -1.77 (0.38), residues: 164
  loop :  0.55 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 147 
 HIS   0.002   0.001   HIS B   4 
 PHE   0.015   0.002   PHE A 144 
 TYR   0.019   0.002   TYR C 213 
 ARG   0.002   0.000   ARG A 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04293 (  544)
  hydrogen bonds       : angle       3.66060 ( 1572)
  covalent geometry    : bond        0.00271 (10672)
  covalent geometry    : angle       0.51240 (14464)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 1.240 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5505 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5496 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5510 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5498 (mpt-90)
  outliers start: 28
  outliers final: 20
  residues processed: 136
  average time/residue: 1.5254
  time to fit residues: 220.5948
Evaluate side-chains
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue    3 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   66 ASP
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    3 SER
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 135 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 45 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  95 GLN
C  95 GLN
D  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.181024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.163993 restraints weight = 8655.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 0.69
r_work: 0.3771 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 2.13 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10672  Z= 0.123
  Angle     :  0.511   7.039  14464  Z= 0.265
  Chirality :  0.040   0.120   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.600  54.891   1484
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.51 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.23), residues: 1364
  helix:  2.38 (0.19), residues: 720
  sheet: -1.79 (0.38), residues: 164
  loop :  0.55 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 147 
 HIS   0.002   0.001   HIS B   4 
 PHE   0.015   0.002   PHE A 144 
 TYR   0.019   0.002   TYR C 213 
 ARG   0.002   0.000   ARG B 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  544)
  hydrogen bonds       : angle       3.66252 ( 1572)
  covalent geometry    : bond        0.00273 (10672)
  covalent geometry    : angle       0.51052 (14464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9208.13 seconds
wall clock time: 162 minutes 20.21 seconds (9740.21 seconds total)