Starting phenix.real_space_refine
on Sun Apr  5 12:07:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ehg_28147/04_2026/8ehg_28147.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ehg_28147/04_2026/8ehg_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_28147/04_2026/8ehg_28147.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ehg_28147/04_2026/8ehg_28147.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ehg_28147/04_2026/8ehg_28147.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ehg_28147/04_2026/8ehg_28147.cif"
  }
  resolution = 2.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/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:
    B, C, D
  Time building chain proxies: 2.11, per 1000 atoms: 0.20
  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: 0.86
  Conformation dependent library (CDL) restraints added in 491.1 milliseconds
  

  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: 0.38
  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: 1.91

  Time building geometry restraints manager: 1.17 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:             12.970
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.640
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.810
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (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
 ARG   0.001   0.000   ARG B 258 
 TYR   0.016   0.002   TYR C 213 
 PHE   0.018   0.002   PHE C 144 
 TRP   0.008   0.002   TRP C 147 
 HIS   0.003   0.001   HIS C 237 

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

*********************** 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  : 0.395 
Fit side-chains
  outliers start: 16
  outliers final: 8
  residues processed: 112
  average time/residue: 0.6998
  time to fit residues: 83.3435
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  : 0.324 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.2980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0970
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.181032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.163356 restraints weight = 8699.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 0.72
r_work: 0.3769 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 2.22 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0619

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= 0.118
  Angle     :  0.496   5.693  14464  Z= 0.259
  Chirality :  0.040   0.119   1644
  Planarity :  0.004   0.024   1880
  Dihedral  :  5.511  56.127   1484
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  7.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.23), residues: 1364
  helix:  2.29 (0.19), residues: 712
  sheet: -1.58 (0.38), residues: 144
  loop :  0.59 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 258 
 TYR   0.017   0.002   TYR C 213 
 PHE   0.015   0.002   PHE C 144 
 TRP   0.005   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10672)
  covalent geometry    : angle       0.49573 (14464)
  hydrogen bonds       : bond        0.04313 (  544)
  hydrogen bonds       : angle       3.82726 ( 1572)

*********************** 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
  148 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 112
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A   34 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6180 (pm20)
REVERT: B   34 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6183 (pm20)
REVERT: C   34 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6180 (pm20)
REVERT: D   34 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6181 (pm20)
  outliers start: 36
  outliers final: 16
  residues processed: 132
  average time/residue: 0.8445
  time to fit residues: 117.2596
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  : 0.443 
-------------------------------------------------------------------------------
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 122 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 118 optimal weight:    0.9990
   chunk 133 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 124 optimal weight:    0.2980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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
A 119 ASN
B  20 HIS
B  95 GLN
B 119 ASN
C  20 HIS
C  95 GLN
C 119 ASN
D  20 HIS
D  95 GLN
D 119 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.178459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.160803 restraints weight = 8688.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 0.71
r_work: 0.3740 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.3654 rms_B_bonded: 2.19 restraints_weight: 0.2500
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.0940

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= 0.134
  Angle     :  0.515   5.572  14464  Z= 0.269
  Chirality :  0.041   0.124   1644
  Planarity :  0.004   0.024   1880
  Dihedral  :  5.679  55.994   1484
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  8.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.22), residues: 1364
  helix:  2.34 (0.19), residues: 712
  sheet: -1.75 (0.36), residues: 164
  loop :  0.58 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 258 
 TYR   0.021   0.002   TYR A 213 
 PHE   0.015   0.002   PHE C 144 
 TRP   0.008   0.002   TRP B 147 
 HIS   0.003   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10672)
  covalent geometry    : angle       0.51496 (14464)
  hydrogen bonds       : bond        0.04643 (  544)
  hydrogen bonds       : angle       3.78476 ( 1572)

*********************** 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
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A   34 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6182 (pm20)
REVERT: A   42 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5384 (mpt-90)
REVERT: B   34 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6181 (pm20)
REVERT: B   42 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5391 (mpt-90)
REVERT: C   34 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6180 (pm20)
REVERT: C   42 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5393 (mpt-90)
REVERT: D   34 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6181 (pm20)
REVERT: D   42 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5395 (mpt-90)
  outliers start: 36
  outliers final: 16
  residues processed: 124
  average time/residue: 0.8369
  time to fit residues: 109.2838
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   42 ARG
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   42 ARG
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   42 ARG
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   42 ARG
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 127 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.175518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.157438 restraints weight = 8668.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 0.73
r_work: 0.3704 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 2.17 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10672  Z= 0.195
  Angle     :  0.597   5.854  14464  Z= 0.315
  Chirality :  0.044   0.137   1644
  Planarity :  0.005   0.027   1880
  Dihedral  :  6.060  55.533   1484
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  :  9.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.22), residues: 1364
  helix:  2.04 (0.18), residues: 712
  sheet: -1.81 (0.37), residues: 164
  loop :  0.50 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 258 
 TYR   0.027   0.003   TYR A 213 
 PHE   0.019   0.003   PHE B 144 
 TRP   0.009   0.002   TRP C 147 
 HIS   0.004   0.001   HIS C   2 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (10672)
  covalent geometry    : angle       0.59740 (14464)
  hydrogen bonds       : bond        0.05480 (  544)
  hydrogen bonds       : angle       3.95766 ( 1572)

*********************** 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
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 92
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7381 (tm-30)
REVERT: A   42 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.5624 (mpt-90)
REVERT: B   14 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7374 (tm-30)
REVERT: B   42 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.5623 (mpt-90)
REVERT: C   14 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7376 (tm-30)
REVERT: C   42 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.5621 (mpt-90)
REVERT: D   14 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7382 (tm-30)
REVERT: D   42 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.5624 (mpt-90)
  outliers start: 40
  outliers final: 20
  residues processed: 124
  average time/residue: 0.8367
  time to fit residues: 109.3008
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   42 ARG
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    3 SER
Chi-restraints excluded: chain B residue   14 GLU
Chi-restraints excluded: chain B residue   42 ARG
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    3 SER
Chi-restraints excluded: chain C residue   14 GLU
Chi-restraints excluded: chain C residue   42 ARG
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    3 SER
Chi-restraints excluded: chain D residue   14 GLU
Chi-restraints excluded: chain D residue   42 ARG
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0770
   chunk 91 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 128 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 127 optimal weight:    3.9990
   overall best weight:    0.7142

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.177696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.159796 restraints weight = 8576.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 0.71
r_work: 0.3753 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3667 rms_B_bonded: 2.19 restraints_weight: 0.2500
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10672  Z= 0.138
  Angle     :  0.524   5.303  14464  Z= 0.275
  Chirality :  0.041   0.128   1644
  Planarity :  0.004   0.024   1880
  Dihedral  :  5.805  54.985   1484
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 10.79 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.22), residues: 1364
  helix:  2.21 (0.18), residues: 712
  sheet: -1.81 (0.37), residues: 164
  loop :  0.55 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 258 
 TYR   0.021   0.002   TYR A 213 
 PHE   0.017   0.002   PHE D 144 
 TRP   0.010   0.002   TRP B 147 
 HIS   0.002   0.001   HIS D   2 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10672)
  covalent geometry    : angle       0.52375 (14464)
  hydrogen bonds       : bond        0.04690 (  544)
  hydrogen bonds       : angle       3.81466 ( 1572)

*********************** 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
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.5493 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5481 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5481 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.5489 (mpt-90)
  outliers start: 36
  outliers final: 20
  residues processed: 120
  average time/residue: 0.8554
  time to fit residues: 108.0594
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  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
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  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   42 ARG
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  169 VAL
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   42 ARG
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  169 VAL
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   42 ARG
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  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 110 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 97 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 85 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.181167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.163466 restraints weight = 8684.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 0.70
r_work: 0.3764 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1048

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= 0.127
  Angle     :  0.509   5.577  14464  Z= 0.266
  Chirality :  0.040   0.123   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.715  54.802   1484
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 10.07 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.22), residues: 1364
  helix:  2.33 (0.19), residues: 712
  sheet: -1.78 (0.38), residues: 164
  loop :  0.60 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 258 
 TYR   0.020   0.002   TYR B 213 
 PHE   0.016   0.002   PHE D 144 
 TRP   0.009   0.002   TRP D 147 
 HIS   0.002   0.001   HIS B   2 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10672)
  covalent geometry    : angle       0.50948 (14464)
  hydrogen bonds       : bond        0.04491 (  544)
  hydrogen bonds       : angle       3.75621 ( 1572)

*********************** 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
  144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 100
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5551 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5546 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5547 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5548 (mpt-90)
  outliers start: 44
  outliers final: 28
  residues processed: 136
  average time/residue: 0.8161
  time to fit residues: 116.9898
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  : 0.323 
-------------------------------------------------------------------------------
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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 64 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 31 optimal weight:    0.1980
   chunk 28 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.177783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.159931 restraints weight = 8580.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 0.71
r_work: 0.3754 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3669 rms_B_bonded: 2.19 restraints_weight: 0.2500
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10672  Z= 0.139
  Angle     :  0.526   5.884  14464  Z= 0.275
  Chirality :  0.041   0.127   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.782  54.880   1484
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 10.16 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.22), residues: 1364
  helix:  2.27 (0.18), residues: 712
  sheet: -1.83 (0.37), residues: 164
  loop :  0.55 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 258 
 TYR   0.022   0.002   TYR B 213 
 PHE   0.017   0.002   PHE B 144 
 TRP   0.009   0.002   TRP D 147 
 HIS   0.002   0.001   HIS B   2 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10672)
  covalent geometry    : angle       0.52620 (14464)
  hydrogen bonds       : bond        0.04692 (  544)
  hydrogen bonds       : angle       3.79744 ( 1572)

*********************** 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
  139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 96
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5488 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5472 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5473 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5480 (mpt-90)
  outliers start: 43
  outliers final: 28
  residues processed: 128
  average time/residue: 0.7972
  time to fit residues: 107.6229
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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 129 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 116 optimal weight:    3.9990
   chunk 115 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.177421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.159467 restraints weight = 8563.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 0.71
r_work: 0.3722 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 2.17 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10672  Z= 0.154
  Angle     :  0.552   7.293  14464  Z= 0.287
  Chirality :  0.042   0.130   1644
  Planarity :  0.004   0.025   1880
  Dihedral  :  5.869  54.796   1484
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 10.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.22), residues: 1364
  helix:  2.15 (0.18), residues: 712
  sheet: -1.85 (0.37), residues: 164
  loop :  0.53 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 258 
 TYR   0.023   0.002   TYR A 213 
 PHE   0.018   0.002   PHE A 144 
 TRP   0.009   0.002   TRP C 147 
 HIS   0.003   0.001   HIS C   2 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10672)
  covalent geometry    : angle       0.55153 (14464)
  hydrogen bonds       : bond        0.04909 (  544)
  hydrogen bonds       : angle       3.84685 ( 1572)

*********************** 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
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5576 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5572 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5575 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5569 (mpt-90)
  outliers start: 36
  outliers final: 28
  residues processed: 124
  average time/residue: 0.8508
  time to fit residues: 111.1552
Evaluate side-chains
  121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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   49 GLU
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  240 THR
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 45 optimal weight:    0.0060
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 115 optimal weight:    0.5980
   chunk 122 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.178494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.160679 restraints weight = 8657.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 0.71
r_work: 0.3763 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 2.20 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1080

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     :  0.514   6.441  14464  Z= 0.268
  Chirality :  0.041   0.124   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.701  54.679   1484
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  9.80 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.22), residues: 1364
  helix:  2.32 (0.19), residues: 712
  sheet: -1.82 (0.38), residues: 164
  loop :  0.59 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 258 
 TYR   0.019   0.002   TYR B 213 
 PHE   0.016   0.002   PHE B 144 
 TRP   0.009   0.002   TRP C 147 
 HIS   0.002   0.001   HIS B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10672)
  covalent geometry    : angle       0.51380 (14464)
  hydrogen bonds       : bond        0.04470 (  544)
  hydrogen bonds       : angle       3.74363 ( 1572)

*********************** 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
  133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5534 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5528 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5514 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.5525 (mpt-90)
  outliers start: 36
  outliers final: 24
  residues processed: 129
  average time/residue: 0.7951
  time to fit residues: 108.4376
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  : 0.355 
-------------------------------------------------------------------------------
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  240 THR
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  240 THR
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  240 THR
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  240 THR
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 41 optimal weight:    0.3980
   chunk 94 optimal weight:    0.4980
   chunk 68 optimal weight:    0.5980
   chunk 131 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 132 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 125 optimal weight:    0.0570
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.180138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.162601 restraints weight = 8583.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 0.70
r_work: 0.3779 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.3695 rms_B_bonded: 2.15 restraints_weight: 0.2500
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10672  Z= 0.113
  Angle     :  0.491   6.226  14464  Z= 0.256
  Chirality :  0.040   0.120   1644
  Planarity :  0.004   0.026   1880
  Dihedral  :  5.543  54.807   1484
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.23), residues: 1364
  helix:  2.40 (0.19), residues: 720
  sheet: -1.78 (0.38), residues: 164
  loop :  0.53 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 258 
 TYR   0.016   0.002   TYR B 213 
 PHE   0.015   0.002   PHE C 144 
 TRP   0.008   0.001   TRP B 147 
 HIS   0.002   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10672)
  covalent geometry    : angle       0.49085 (14464)
  hydrogen bonds       : bond        0.04116 (  544)
  hydrogen bonds       : angle       3.65165 ( 1572)

********************** 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
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5538 (mpt-90)
REVERT: B   42 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5530 (mpt-90)
REVERT: C   42 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5528 (mpt-90)
REVERT: D   42 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.5524 (mpt-90)
  outliers start: 24
  outliers final: 20
  residues processed: 128
  average time/residue: 0.8703
  time to fit residues: 117.2219
Evaluate side-chains
  136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
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 87 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0770
   chunk 73 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 21 optimal weight:    0.1980
   chunk 67 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.181350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.164000 restraints weight = 8653.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 0.70
r_work: 0.3753 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1173

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= 0.122
  Angle     :  0.516   8.644  14464  Z= 0.266
  Chirality :  0.040   0.120   1644
  Planarity :  0.004   0.027   1880
  Dihedral  :  5.575  54.782   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 :  2.16 %
    Allowed  : 10.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.23), residues: 1364
  helix:  2.37 (0.19), residues: 720
  sheet: -1.75 (0.38), residues: 164
  loop :  0.57 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 258 
 TYR   0.018   0.002   TYR A 213 
 PHE   0.015   0.002   PHE A 144 
 TRP   0.009   0.002   TRP C 147 
 HIS   0.002   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10672)
  covalent geometry    : angle       0.51574 (14464)
  hydrogen bonds       : bond        0.04245 (  544)
  hydrogen bonds       : angle       3.67406 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4327.59 seconds
wall clock time: 74 minutes 38.12 seconds (4478.12 seconds total)