Starting phenix.real_space_refine
on Wed Mar  4 08:57:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d64_27216/03_2026/8d64_27216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d64_27216/03_2026/8d64_27216.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d64_27216/03_2026/8d64_27216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d64_27216/03_2026/8d64_27216.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d64_27216/03_2026/8d64_27216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d64_27216/03_2026/8d64_27216.map"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
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      35      5.16       5
     C    8175      2.51       5
     N    2085      2.21       5
     O    2250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12545
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'DHL': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 2.06, per 1000 atoms: 0.16
  Number of scatterers: 12545
  At special positions: 0
  Unit cell: (90.2, 90.2, 123.2, 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      35     16.00
     O    2250      8.00
     N    2085      7.00
     C    8175      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 509.3 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 15 sheets defined
      32.5% alpha, 36.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 69
      removed outlier: 3.654A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN A  69 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 249
    Processing helix  chain 'A' and resid 260 through 286
    Processing helix  chain 'A' and resid 302 through 317
    Processing helix  chain 'B' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN B  69 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU B 212 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 249
    Processing helix  chain 'B' and resid 260 through 286
    Processing helix  chain 'B' and resid 302 through 317
    Processing helix  chain 'C' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN C  69 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 249
    Processing helix  chain 'C' and resid 260 through 286
    Processing helix  chain 'C' and resid 302 through 317
    Processing helix  chain 'D' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASN D  69 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
      removed outlier: 3.530A  pdb=" N   LEU D 212 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 249
    Processing helix  chain 'D' and resid 260 through 286
    Processing helix  chain 'D' and resid 302 through 317
    Processing helix  chain 'E' and resid 62 through 69
      removed outlier: 3.653A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN E  69 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
      removed outlier: 3.531A  pdb=" N   LEU E 212 " --> pdb=" O   PHE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 249
    Processing helix  chain 'E' and resid 260 through 286
    Processing helix  chain 'E' and resid 302 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 5.294A  pdb=" N   THR A  87 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU A 107 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   ASN A  89 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   THR A  32 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   VAL A  26 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   TYR A  38 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE A  20 " --> pdb=" O   TYR A  38 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   VAL A  40 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN A  42 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL A  16 " --> pdb=" O   GLN A  42 " (cutoff:3.500A)
      removed outlier: 8.728A  pdb=" N   THR A  44 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL A  14 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58
      removed outlier: 5.293A  pdb=" N   THR B  87 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU B 107 " --> pdb=" O   THR B  87 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   ASN B  89 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR B  32 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   VAL B  26 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   TYR B  38 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE B  20 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL B  40 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN B  42 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL B  16 " --> pdb=" O   GLN B  42 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   THR B  44 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   VAL B  14 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58
      removed outlier: 5.293A  pdb=" N   THR C  87 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU C 107 " --> pdb=" O   THR C  87 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASN C  89 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL C  26 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   TYR C  38 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE C  20 " --> pdb=" O   TYR C  38 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL C  40 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN C  42 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   VAL C  16 " --> pdb=" O   GLN C  42 " (cutoff:3.500A)
      removed outlier: 8.728A  pdb=" N   THR C  44 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL C  14 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58
      removed outlier: 5.294A  pdb=" N   THR D  87 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU D 107 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASN D  89 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR D  32 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL D  26 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   TYR D  38 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ILE D  20 " --> pdb=" O   TYR D  38 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   VAL D  40 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN D  42 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL D  16 " --> pdb=" O   GLN D  42 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   THR D  44 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL D  14 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.522A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.522A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58
      removed outlier: 5.293A  pdb=" N   THR E  87 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU E 107 " --> pdb=" O   THR E  87 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASN E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR E  32 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   VAL E  26 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   TYR E  38 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE E  20 " --> pdb=" O   TYR E  38 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL E  40 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLN E  42 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   VAL E  16 " --> pdb=" O   GLN E  42 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   THR E  44 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL E  14 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.521A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1830 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: 2.08

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3947
        1.34 -     1.46: 2403
        1.46 -     1.57: 6475
        1.57 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" N   ASP D 158 "
       pdb=" CA  ASP D 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 6.30e-03 2.52e+04 2.20e+01
  bond pdb=" N   ASP E 158 "
       pdb=" CA  ASP E 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.029 6.30e-03 2.52e+04 2.19e+01
  bond pdb=" N   ASP A 158 "
       pdb=" CA  ASP A 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.029 6.30e-03 2.52e+04 2.15e+01
  bond pdb=" N   ASP B 158 "
       pdb=" CA  ASP B 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 6.30e-03 2.52e+04 2.11e+01
  bond pdb=" N   ASP C 158 "
       pdb=" CA  ASP C 158 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 6.30e-03 2.52e+04 2.08e+01
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 16567
        1.52 -     3.05: 802
        3.05 -     4.57: 121
        4.57 -     6.10: 25
        6.10 -     7.62: 30
  Bond angle restraints: 17545
  Sorted by residual:
  angle pdb=" C   ASP B 158 "
        pdb=" CA  ASP B 158 "
        pdb=" CB  ASP B 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.76    5.78 1.46e+00 4.69e-01 1.57e+01
  angle pdb=" C   ASP E 158 "
        pdb=" CA  ASP E 158 "
        pdb=" CB  ASP E 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.79    5.75 1.46e+00 4.69e-01 1.55e+01
  angle pdb=" C   ASP C 158 "
        pdb=" CA  ASP C 158 "
        pdb=" CB  ASP C 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.80    5.74 1.46e+00 4.69e-01 1.55e+01
  angle pdb=" C   ASP A 158 "
        pdb=" CA  ASP A 158 "
        pdb=" CB  ASP A 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.81    5.73 1.46e+00 4.69e-01 1.54e+01
  angle pdb=" C   ASP D 158 "
        pdb=" CA  ASP D 158 "
        pdb=" CB  ASP D 158 "
      ideal   model   delta    sigma   weight residual
     116.54  110.82    5.72 1.46e+00 4.69e-01 1.54e+01
  ... (remaining 17540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 6702
       16.95 -    33.89: 703
       33.89 -    50.84: 100
       50.84 -    67.78: 15
       67.78 -    84.73: 10
  Dihedral angle restraints: 7530
    sinusoidal: 3025
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  LEU C 118 "
           pdb=" C   LEU C 118 "
           pdb=" N   PHE C 119 "
           pdb=" CA  PHE C 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.43  -28.57     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  LEU E 118 "
           pdb=" C   LEU E 118 "
           pdb=" N   PHE E 119 "
           pdb=" CA  PHE E 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.45  -28.55     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  LEU A 118 "
           pdb=" C   LEU A 118 "
           pdb=" N   PHE A 119 "
           pdb=" CA  PHE A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.45  -28.55     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1323
       0.050 -    0.100: 453
       0.100 -    0.150: 137
       0.150 -    0.200: 26
       0.200 -    0.250: 11
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CA  GLU B 156 "
            pdb=" N   GLU B 156 "
            pdb=" C   GLU B 156 "
            pdb=" CB  GLU B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  GLU A 156 "
            pdb=" N   GLU A 156 "
            pdb=" C   GLU A 156 "
            pdb=" CB  GLU A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  GLU E 156 "
            pdb=" N   GLU E 156 "
            pdb=" C   GLU E 156 "
            pdb=" CB  GLU E 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D  54 "    0.039 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO D  55 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO D  55 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D  55 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  54 "   -0.039 5.00e-02 4.00e+02   5.87e-02 5.52e+00
        pdb=" N   PRO C  55 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E  54 "    0.039 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO E  55 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO E  55 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO E  55 "    0.033 5.00e-02 4.00e+02
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3289
        2.80 -     3.32: 10426
        3.32 -     3.85: 20050
        3.85 -     4.37: 24068
        4.37 -     4.90: 43065
  Nonbonded interactions: 100898
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  59 "
            pdb=" OG  SER B 134 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG  SER A 227 "
            pdb=" CG  GLU A 230 "
     model   vdw
     2.289 3.440
  nonbonded pdb=" OG  SER C 227 "
            pdb=" CG  GLU C 230 "
     model   vdw
     2.289 3.440
  nonbonded pdb=" OG  SER E 227 "
            pdb=" CG  GLU E 230 "
     model   vdw
     2.289 3.440
  nonbonded pdb=" OG  SER B 227 "
            pdb=" CG  GLU B 230 "
     model   vdw
     2.289 3.440
  ... (remaining 100893 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.970
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
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      :  0.007   0.045  12880  Z= 0.331
  Angle     :  0.809   7.624  17545  Z= 0.470
  Chirality :  0.058   0.250   1950
  Planarity :  0.006   0.059   2235
  Dihedral  : 13.690  84.726   4620
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.61 (0.18), residues: 1525
  helix: -1.79 (0.18), residues: 535
  sheet: -1.46 (0.22), residues: 505
  loop : -3.92 (0.20), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 123 
 TYR   0.016   0.002   TYR B 245 
 PHE   0.014   0.002   PHE C 106 
 TRP   0.018   0.002   TRP C 206 
 HIS   0.005   0.001   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00709 (12880)
  covalent geometry    : angle       0.80887 (17545)
  hydrogen bonds       : bond        0.11028 (  575)
  hydrogen bonds       : angle       5.98952 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.537 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.8893 (m-80) cc_final: 0.8509 (m-80)
REVERT: B  131 GLU cc_start: 0.8793 (tt0) cc_final: 0.8481 (tt0)
REVERT: C   38 TYR cc_start: 0.8912 (m-80) cc_final: 0.8611 (m-80)
REVERT: C   90 LYS cc_start: 0.8893 (pttt) cc_final: 0.8600 (pttm)
REVERT: C  146 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7878 (mm-40)
REVERT: D   38 TYR cc_start: 0.8771 (m-80) cc_final: 0.8506 (m-80)
REVERT: E   65 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8266 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.1220
  time to fit residues: 33.1492
Evaluate side-chains
  121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 139 GLN
A 182 GLN
B 139 GLN
C 139 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.148530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.108344 restraints weight = 14388.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.37
r_work: 0.2950 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  12880  Z= 0.144
  Angle     :  0.568   5.968  17545  Z= 0.298
  Chirality :  0.047   0.146   1950
  Planarity :  0.005   0.048   2235
  Dihedral  :  5.123  22.676   1690
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.56 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.20), residues: 1525
  helix: -0.04 (0.21), residues: 510
  sheet: -0.71 (0.26), residues: 425
  loop : -3.25 (0.20), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 123 
 TYR   0.013   0.001   TYR A 245 
 PHE   0.013   0.001   PHE D 247 
 TRP   0.015   0.001   TRP B 206 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (12880)
  covalent geometry    : angle       0.56788 (17545)
  hydrogen bonds       : bond        0.04025 (  575)
  hydrogen bonds       : angle       4.50849 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.9203 (ptpp) cc_final: 0.8991 (pttm)
REVERT: B   38 TYR cc_start: 0.9191 (m-80) cc_final: 0.8878 (m-80)
REVERT: C   38 TYR cc_start: 0.9154 (m-80) cc_final: 0.8842 (m-80)
REVERT: C   90 LYS cc_start: 0.9174 (pttt) cc_final: 0.8913 (pttm)
REVERT: C  146 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8421 (mm-40)
REVERT: D   38 TYR cc_start: 0.9112 (m-80) cc_final: 0.8842 (m-80)
REVERT: D   65 ARG cc_start: 0.8520 (mtp-110) cc_final: 0.8288 (mtm110)
REVERT: E   65 ARG cc_start: 0.8865 (mtp-110) cc_final: 0.8658 (mtm110)
REVERT: E  224 TRP cc_start: 0.7413 (m100) cc_final: 0.7193 (m-90)
  outliers start: 30
  outliers final: 25
  residues processed: 174
  average time/residue: 0.1039
  time to fit residues: 26.2376
Evaluate side-chains
  153 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 7 optimal weight:    0.4980
   chunk 147 optimal weight:    0.9980
   chunk 130 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    2.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.147474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.107119 restraints weight = 14520.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.36
r_work: 0.2922 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12880  Z= 0.169
  Angle     :  0.562   5.922  17545  Z= 0.293
  Chirality :  0.048   0.143   1950
  Planarity :  0.004   0.045   2235
  Dihedral  :  5.105  23.352   1690
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.60 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.21), residues: 1525
  helix:  0.93 (0.22), residues: 500
  sheet: -0.42 (0.28), residues: 395
  loop : -2.89 (0.21), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 123 
 TYR   0.016   0.001   TYR C 245 
 PHE   0.014   0.001   PHE D 247 
 TRP   0.015   0.001   TRP E 206 
 HIS   0.005   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12880)
  covalent geometry    : angle       0.56154 (17545)
  hydrogen bonds       : bond        0.03923 (  575)
  hydrogen bonds       : angle       4.38468 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.487 
Fit side-chains
REVERT: B   38 TYR cc_start: 0.9178 (m-80) cc_final: 0.8894 (m-80)
REVERT: C   38 TYR cc_start: 0.9144 (m-80) cc_final: 0.8832 (m-80)
REVERT: C   90 LYS cc_start: 0.9145 (pttt) cc_final: 0.8860 (pttm)
REVERT: C  146 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8414 (mm-40)
REVERT: D   38 TYR cc_start: 0.9142 (m-80) cc_final: 0.8878 (m-80)
REVERT: D   65 ARG cc_start: 0.8722 (mtp-110) cc_final: 0.8503 (mtm110)
  outliers start: 33
  outliers final: 30
  residues processed: 159
  average time/residue: 0.1149
  time to fit residues: 26.1676
Evaluate side-chains
  161 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   chunk 143 optimal weight:    7.9990
   chunk 96 optimal weight:    4.9990
   chunk 147 optimal weight:    0.2980
   chunk 117 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 144 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 133 optimal weight:    3.9990
   overall best weight:    2.4588

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.147175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.111860 restraints weight = 14363.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.40
r_work: 0.2927 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  12880  Z= 0.190
  Angle     :  0.579   5.887  17545  Z= 0.302
  Chirality :  0.048   0.145   1950
  Planarity :  0.004   0.044   2235
  Dihedral  :  5.124  24.449   1690
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.91 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.11 (0.22), residues: 1525
  helix:  0.99 (0.23), residues: 530
  sheet: -0.41 (0.28), residues: 410
  loop : -2.66 (0.22), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 123 
 TYR   0.016   0.002   TYR C 245 
 PHE   0.015   0.002   PHE D 247 
 TRP   0.016   0.001   TRP E 206 
 HIS   0.006   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (12880)
  covalent geometry    : angle       0.57858 (17545)
  hydrogen bonds       : bond        0.04010 (  575)
  hydrogen bonds       : angle       4.36474 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 TYR cc_start: 0.9167 (m-80) cc_final: 0.8912 (m-80)
REVERT: B  287 GLN cc_start: 0.0937 (OUTLIER) cc_final: 0.0612 (mm110)
REVERT: C   38 TYR cc_start: 0.9128 (m-80) cc_final: 0.8846 (m-80)
REVERT: C  146 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8413 (mm-40)
REVERT: D   38 TYR cc_start: 0.9110 (m-80) cc_final: 0.8902 (m-80)
REVERT: D   65 ARG cc_start: 0.8741 (mtp-110) cc_final: 0.8530 (mtm110)
REVERT: E  287 GLN cc_start: 0.1133 (OUTLIER) cc_final: 0.0068 (mm110)
  outliers start: 40
  outliers final: 31
  residues processed: 172
  average time/residue: 0.1062
  time to fit residues: 26.7598
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 139 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 139 GLN
B  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.145096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.104846 restraints weight = 14510.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.36
r_work: 0.2921 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  12880  Z= 0.235
  Angle     :  0.615   6.015  17545  Z= 0.321
  Chirality :  0.050   0.146   1950
  Planarity :  0.005   0.046   2235
  Dihedral  :  5.315  26.373   1690
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.22 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.10 (0.22), residues: 1525
  helix:  1.08 (0.23), residues: 530
  sheet: -0.40 (0.27), residues: 440
  loop : -2.87 (0.22), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 123 
 TYR   0.019   0.002   TYR C 245 
 PHE   0.016   0.002   PHE B 247 
 TRP   0.024   0.002   TRP E 224 
 HIS   0.007   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 (12880)
  covalent geometry    : angle       0.61539 (17545)
  hydrogen bonds       : bond        0.04377 (  575)
  hydrogen bonds       : angle       4.47932 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 139
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.8887 (tp)
REVERT: B   38 TYR cc_start: 0.9184 (m-80) cc_final: 0.8921 (m-80)
REVERT: B  145 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.8912 (tp)
REVERT: B  287 GLN cc_start: 0.0755 (OUTLIER) cc_final: 0.0431 (mm110)
REVERT: C   38 TYR cc_start: 0.9158 (m-80) cc_final: 0.8869 (m-80)
REVERT: C  146 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8417 (mm-40)
REVERT: D   38 TYR cc_start: 0.9154 (m-80) cc_final: 0.8939 (m-80)
REVERT: D  145 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9133 (tp)
REVERT: E  287 GLN cc_start: 0.1023 (OUTLIER) cc_final: -0.0030 (mm110)
  outliers start: 41
  outliers final: 32
  residues processed: 168
  average time/residue: 0.0993
  time to fit residues: 24.6965
Evaluate side-chains
  172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 120 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0070
   chunk 56 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.9804

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 182 GLN
B  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.148525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.122872 restraints weight = 14279.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 0.78
r_work: 0.3047 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12880  Z= 0.161
  Angle     :  0.558   5.756  17545  Z= 0.290
  Chirality :  0.047   0.145   1950
  Planarity :  0.004   0.042   2235
  Dihedral  :  5.044  23.690   1690
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.07 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.22), residues: 1525
  helix:  1.25 (0.23), residues: 530
  sheet: -0.20 (0.27), residues: 440
  loop : -2.81 (0.22), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  65 
 TYR   0.016   0.001   TYR C 245 
 PHE   0.013   0.001   PHE C 247 
 TRP   0.017   0.001   TRP B 206 
 HIS   0.005   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (12880)
  covalent geometry    : angle       0.55809 (17545)
  hydrogen bonds       : bond        0.03822 (  575)
  hydrogen bonds       : angle       4.29797 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 144
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.8822 (tp)
REVERT: B   38 TYR cc_start: 0.9058 (m-80) cc_final: 0.8795 (m-80)
REVERT: B  145 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.8856 (tp)
REVERT: B  287 GLN cc_start: 0.1180 (OUTLIER) cc_final: 0.0822 (mm110)
REVERT: C   38 TYR cc_start: 0.9033 (m-80) cc_final: 0.8766 (m-80)
REVERT: C  146 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8294 (mm-40)
REVERT: D   38 TYR cc_start: 0.9015 (m-80) cc_final: 0.8791 (m-80)
REVERT: D  145 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9087 (tp)
REVERT: D  309 LEU cc_start: 0.2124 (OUTLIER) cc_final: 0.1921 (pt)
REVERT: E  145 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.8856 (tp)
REVERT: E  182 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7878 (mp10)
REVERT: E  287 GLN cc_start: 0.1468 (OUTLIER) cc_final: 0.0312 (mm110)
  outliers start: 43
  outliers final: 30
  residues processed: 176
  average time/residue: 0.1033
  time to fit residues: 26.6005
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 142
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  182 GLN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 117 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 120 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.149603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.123236 restraints weight = 14204.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 0.79
r_work: 0.3024 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 2.30 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12880  Z= 0.148
  Angle     :  0.544   5.954  17545  Z= 0.282
  Chirality :  0.047   0.145   1950
  Planarity :  0.004   0.040   2235
  Dihedral  :  4.891  22.287   1690
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.09 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.22), residues: 1525
  helix:  1.41 (0.23), residues: 530
  sheet:  0.37 (0.26), residues: 475
  loop : -3.13 (0.22), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 123 
 TYR   0.014   0.001   TYR C 245 
 PHE   0.012   0.001   PHE C 247 
 TRP   0.017   0.001   TRP B 206 
 HIS   0.004   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12880)
  covalent geometry    : angle       0.54415 (17545)
  hydrogen bonds       : bond        0.03615 (  575)
  hydrogen bonds       : angle       4.19809 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.8858 (tp)
REVERT: B   38 TYR cc_start: 0.9050 (m-80) cc_final: 0.8785 (m-80)
REVERT: B  145 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.8856 (tp)
REVERT: B  287 GLN cc_start: 0.1245 (OUTLIER) cc_final: 0.0888 (mm110)
REVERT: C   38 TYR cc_start: 0.9027 (m-80) cc_final: 0.8741 (m-80)
REVERT: C  146 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8259 (mm-40)
REVERT: D   38 TYR cc_start: 0.9019 (m-80) cc_final: 0.8795 (m-80)
REVERT: D  145 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9066 (tp)
REVERT: D  239 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7557 (mtt)
REVERT: E  145 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.8856 (tp)
REVERT: E  287 GLN cc_start: 0.1544 (OUTLIER) cc_final: 0.0373 (mm110)
  outliers start: 39
  outliers final: 31
  residues processed: 175
  average time/residue: 0.1044
  time to fit residues: 27.0843
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 142
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  239 MET
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 139 optimal weight:    3.9990
   chunk 107 optimal weight:    0.4980
   chunk 14 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    2.8988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.144975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.105805 restraints weight = 14393.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.28
r_work: 0.2910 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12880  Z= 0.215
  Angle     :  0.597   5.915  17545  Z= 0.310
  Chirality :  0.049   0.145   1950
  Planarity :  0.005   0.043   2235
  Dihedral  :  5.149  25.390   1690
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.80 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.22), residues: 1525
  helix:  1.32 (0.23), residues: 530
  sheet:  0.34 (0.25), residues: 475
  loop : -3.15 (0.22), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 123 
 TYR   0.018   0.002   TYR C 245 
 PHE   0.015   0.002   PHE C 247 
 TRP   0.016   0.002   TRP A 206 
 HIS   0.006   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 (12880)
  covalent geometry    : angle       0.59691 (17545)
  hydrogen bonds       : bond        0.04143 (  575)
  hydrogen bonds       : angle       4.36775 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 138
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.8885 (tp)
REVERT: B   38 TYR cc_start: 0.9179 (m-80) cc_final: 0.8935 (m-80)
REVERT: B  124 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7712 (mm-40)
REVERT: B  145 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.8889 (tp)
REVERT: B  287 GLN cc_start: 0.0839 (OUTLIER) cc_final: 0.0524 (mm110)
REVERT: C   38 TYR cc_start: 0.9157 (m-80) cc_final: 0.8852 (m-80)
REVERT: C  146 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8401 (mm-40)
REVERT: D   38 TYR cc_start: 0.9160 (m-80) cc_final: 0.8935 (m-80)
REVERT: D  145 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9102 (tp)
REVERT: D  287 GLN cc_start: 0.1280 (OUTLIER) cc_final: 0.0840 (mm110)
REVERT: E  145 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.8918 (tp)
REVERT: E  182 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7771 (mp10)
REVERT: E  287 GLN cc_start: 0.1098 (OUTLIER) cc_final: 0.0068 (mm110)
  outliers start: 49
  outliers final: 36
  residues processed: 175
  average time/residue: 0.1077
  time to fit residues: 27.8178
Evaluate side-chains
  182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 137
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  187 GLU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  136 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  136 ASN
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  184 ASN
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  182 GLN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 136 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.151052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 112)---------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.113591 restraints weight = 14349.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.21
r_work: 0.2983 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  12880  Z= 0.120
  Angle     :  0.548  17.734  17545  Z= 0.278
  Chirality :  0.046   0.145   1950
  Planarity :  0.004   0.040   2235
  Dihedral  :  4.781  20.982   1690
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.67 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.22), residues: 1525
  helix:  1.43 (0.23), residues: 530
  sheet:  0.55 (0.26), residues: 475
  loop : -3.09 (0.22), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 123 
 TYR   0.011   0.001   TYR C 245 
 PHE   0.011   0.001   PHE E 106 
 TRP   0.018   0.001   TRP B 206 
 HIS   0.004   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12880)
  covalent geometry    : angle       0.54771 (17545)
  hydrogen bonds       : bond        0.03440 (  575)
  hydrogen bonds       : angle       4.12456 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 147
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.8823 (tp)
REVERT: B   38 TYR cc_start: 0.9114 (m-80) cc_final: 0.8795 (m-80)
REVERT: B  145 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.8825 (tp)
REVERT: B  287 GLN cc_start: 0.0810 (OUTLIER) cc_final: 0.0510 (mm110)
REVERT: C   38 TYR cc_start: 0.9106 (m-80) cc_final: 0.8758 (m-80)
REVERT: C  146 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8332 (mm-40)
REVERT: D   38 TYR cc_start: 0.9087 (m-80) cc_final: 0.8827 (m-80)
REVERT: D  145 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9020 (tp)
REVERT: D  287 GLN cc_start: 0.1245 (OUTLIER) cc_final: 0.0806 (mm110)
REVERT: E  145 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.8831 (tp)
REVERT: E  182 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7802 (mp10)
REVERT: E  287 GLN cc_start: 0.1072 (OUTLIER) cc_final: 0.0119 (mm110)
  outliers start: 42
  outliers final: 31
  residues processed: 178
  average time/residue: 0.0988
  time to fit residues: 26.2252
Evaluate side-chains
  183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 144
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  184 ASN
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  184 ASN
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  182 GLN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 119 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 112 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.150192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.124413 restraints weight = 14241.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 0.79
r_work: 0.3050 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12880  Z= 0.147
  Angle     :  0.563  13.891  17545  Z= 0.288
  Chirality :  0.047   0.186   1950
  Planarity :  0.004   0.054   2235
  Dihedral  :  4.832  21.779   1690
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.33 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.22), residues: 1525
  helix:  1.45 (0.23), residues: 530
  sheet:  0.61 (0.26), residues: 470
  loop : -3.04 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 123 
 TYR   0.013   0.001   TYR C 245 
 PHE   0.013   0.001   PHE D 308 
 TRP   0.017   0.001   TRP B 206 
 HIS   0.004   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12880)
  covalent geometry    : angle       0.56272 (17545)
  hydrogen bonds       : bond        0.03606 (  575)
  hydrogen bonds       : angle       4.14166 ( 1830)

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

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  145 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.8847 (tp)
REVERT: A  287 GLN cc_start: 0.1197 (OUTLIER) cc_final: 0.0449 (mm110)
REVERT: B   38 TYR cc_start: 0.9031 (m-80) cc_final: 0.8775 (m-80)
REVERT: B  145 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.8862 (tp)
REVERT: B  287 GLN cc_start: 0.1164 (OUTLIER) cc_final: 0.0815 (mm110)
REVERT: C   38 TYR cc_start: 0.9028 (m-80) cc_final: 0.8769 (m-80)
REVERT: C  146 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8294 (mm-40)
REVERT: D   38 TYR cc_start: 0.9022 (m-80) cc_final: 0.8801 (m-80)
REVERT: D  145 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9056 (tp)
REVERT: D  287 GLN cc_start: 0.1580 (OUTLIER) cc_final: 0.1083 (mm110)
REVERT: E  145 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.8876 (tp)
REVERT: E  182 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7889 (mp10)
REVERT: E  287 GLN cc_start: 0.1452 (OUTLIER) cc_final: 0.0469 (mm110)
  outliers start: 42
  outliers final: 32
  residues processed: 177
  average time/residue: 0.0979
  time to fit residues: 25.6059
Evaluate side-chains
  185 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  287 GLN
Chi-restraints excluded: chain C residue  113 ASP
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  184 ASN
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  281 ILE
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain D residue   30 GLU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  184 ASN
Chi-restraints excluded: chain D residue  237 THR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  281 ILE
Chi-restraints excluded: chain D residue  287 GLN
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue  136 ASN
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  182 GLN
Chi-restraints excluded: chain E residue  281 ILE
Chi-restraints excluded: chain E residue  287 GLN
Chi-restraints excluded: chain E residue  304 PHE
Chi-restraints excluded: chain E residue  309 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0870
   chunk 63 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 141 optimal weight:    0.8980
   chunk 96 optimal weight:    0.0670
   chunk 51 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7898

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.154285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 101)---------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.117564 restraints weight = 14264.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 1.19
r_work: 0.3035 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12880  Z= 0.103
  Angle     :  0.525  14.313  17545  Z= 0.266
  Chirality :  0.046   0.161   1950
  Planarity :  0.004   0.050   2235
  Dihedral  :  4.514  19.077   1690
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.69 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.22), residues: 1525
  helix:  1.53 (0.23), residues: 540
  sheet:  0.78 (0.26), residues: 470
  loop : -3.10 (0.22), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 123 
 TYR   0.007   0.001   TYR C 245 
 PHE   0.011   0.001   PHE E 106 
 TRP   0.018   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (12880)
  covalent geometry    : angle       0.52480 (17545)
  hydrogen bonds       : bond        0.03127 (  575)
  hydrogen bonds       : angle       3.97076 ( 1830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2814.77 seconds
wall clock time: 48 minutes 46.53 seconds (2926.53 seconds total)