Starting phenix.real_space_refine
on Sat Aug 23 13:13:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f34_28831/08_2025/8f34_28831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f34_28831/08_2025/8f34_28831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f34_28831/08_2025/8f34_28831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f34_28831/08_2025/8f34_28831.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f34_28831/08_2025/8f34_28831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f34_28831/08_2025/8f34_28831.map"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      30      5.16       5
     C    8180      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 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12545
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "E"
      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: "E"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    D, C, B, A
  Time building chain proxies: 2.00, per 1000 atoms: 0.16
  Number of scatterers: 12545
  At special positions: 0
  Unit cell: (88.038, 88.038, 122.859, 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      30     16.00
     O    2250      8.00
     N    2085      7.00
     C    8180      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: 1.08
  Conformation dependent library (CDL) restraints added in 554.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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 10 sheets defined
      31.3% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.864A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU E 212 " --> pdb=" O   PHE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 225
    Processing helix  chain 'E' and resid 227 through 245
    Processing helix  chain 'E' and resid 260 through 286
    Processing helix  chain 'E' and resid 303 through 317
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.864A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU D 212 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 227 through 245
    Processing helix  chain 'D' and resid 260 through 286
    Processing helix  chain 'D' and resid 303 through 317
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.863A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 227 through 245
    Processing helix  chain 'C' and resid 260 through 286
    Processing helix  chain 'C' and resid 303 through 317
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.863A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU B 212 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 227 through 245
    Processing helix  chain 'B' and resid 260 through 286
    Processing helix  chain 'B' and resid 303 through 317
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.864A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
      removed outlier: 3.819A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 227 through 245
    Processing helix  chain 'A' and resid 260 through 286
    Processing helix  chain 'A' and resid 303 through 317
    Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER E  84 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU E 107 " --> pdb=" O   SER E  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP E  86 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG E 105 " --> pdb=" O   ASP E  86 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   GLY E  88 " --> pdb=" O   ASN E 103 " (cutoff:3.500A)
      removed outlier: 10.358A  pdb=" N   ASN E 103 " --> pdb=" O   GLY E  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS E  90 " --> pdb=" O   ILE E 101 " (cutoff:3.500A)
      removed outlier: 11.161A  pdb=" N   ILE E 101 " --> pdb=" O   LYS E  90 " (cutoff:3.500A)
      removed outlier: 9.870A  pdb=" N   LEU E  92 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG E  99 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.628A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE E 188 " --> pdb=" O   SER E 171 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER E 171 " --> pdb=" O   PHE E 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG E 190 " --> pdb=" O   HIS E 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS E 169 " --> pdb=" O   ARG E 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR E 192 " --> pdb=" O   SER E 167 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER E 167 " --> pdb=" O   THR E 192 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ARG E 194 " --> pdb=" O   LYS E 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS E 165 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP E 196 " --> pdb=" O   ARG E 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER D  84 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   LEU D 107 " --> pdb=" O   SER D  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP D  86 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG D 105 " --> pdb=" O   ASP D  86 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLY D  88 " --> pdb=" O   ASN D 103 " (cutoff:3.500A)
      removed outlier: 10.359A  pdb=" N   ASN D 103 " --> pdb=" O   GLY D  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS D  90 " --> pdb=" O   ILE D 101 " (cutoff:3.500A)
      removed outlier: 11.161A  pdb=" N   ILE D 101 " --> pdb=" O   LYS D  90 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   LEU D  92 " --> pdb=" O   ARG D  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG D  99 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.565A  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: 6.665A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.628A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE D 188 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   SER D 171 " --> pdb=" O   PHE D 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG D 190 " --> pdb=" O   HIS D 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS D 169 " --> pdb=" O   ARG D 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR D 192 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER D 167 " --> pdb=" O   THR D 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG D 194 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS D 165 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP D 196 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER C  84 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU C 107 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP C  86 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG C 105 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   GLY C  88 " --> pdb=" O   ASN C 103 " (cutoff:3.500A)
      removed outlier: 10.357A  pdb=" N   ASN C 103 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS C  90 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
      removed outlier: 11.162A  pdb=" N   ILE C 101 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   LEU C  92 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG C  99 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.564A  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: 6.664A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.629A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE C 188 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER C 171 " --> pdb=" O   PHE C 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG C 190 " --> pdb=" O   HIS C 169 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   HIS C 169 " --> pdb=" O   ARG C 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR C 192 " --> pdb=" O   SER C 167 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   SER C 167 " --> pdb=" O   THR C 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG C 194 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   LYS C 165 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP C 196 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   SER B  84 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LEU B 107 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP B  86 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ARG B 105 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 10.357A  pdb=" N   ASN B 103 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 9.936A  pdb=" N   LYS B  90 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 11.162A  pdb=" N   ILE B 101 " --> pdb=" O   LYS B  90 " (cutoff:3.500A)
      removed outlier: 9.870A  pdb=" N   LEU B  92 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG B  99 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.564A  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: 6.665A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.628A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE B 188 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   SER B 171 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG B 190 " --> pdb=" O   HIS B 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS B 169 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR B 192 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER B 167 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG B 194 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS B 165 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP B 196 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.289A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   SER A  84 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   LEU A 107 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP A  86 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG A 105 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLY A  88 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 10.358A  pdb=" N   ASN A 103 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 9.935A  pdb=" N   LYS A  90 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 11.160A  pdb=" N   ILE A 101 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   LEU A  92 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
      removed outlier: 10.904A  pdb=" N   ARG A  99 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.564A  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: 6.665A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.629A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   PHE A 188 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   SER A 171 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ARG A 190 " --> pdb=" O   HIS A 169 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   HIS A 169 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR A 192 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER A 167 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG A 194 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS A 165 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP A 196 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)

    530 hydrogen bonds defined for protein.
    1545 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.44 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: 3892
        1.34 -     1.46: 2331
        1.46 -     1.57: 6607
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" CA  TRP C 160 "
       pdb=" C   TRP C 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.020 1.03e-02 9.43e+03 3.64e+00
  bond pdb=" CA  TRP E 160 "
       pdb=" C   TRP E 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.46e+00
  bond pdb=" CA  TRP A 160 "
       pdb=" C   TRP A 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.43e+00
  bond pdb=" CA  TRP B 160 "
       pdb=" C   TRP B 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.40e+00
  bond pdb=" CA  TRP D 160 "
       pdb=" C   TRP D 160 "
    ideal  model  delta    sigma   weight residual
    1.526  1.507  0.019 1.03e-02 9.43e+03 3.39e+00
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 16973
        1.86 -     3.72: 477
        3.72 -     5.58: 50
        5.58 -     7.45: 35
        7.45 -     9.31: 10
  Bond angle restraints: 17545
  Sorted by residual:
  angle pdb=" C   ASN B  60 "
        pdb=" N   THR B  61 "
        pdb=" CA  THR B  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.85   -9.31 1.91e+00 2.74e-01 2.37e+01
  angle pdb=" C   ASN E  60 "
        pdb=" N   THR E  61 "
        pdb=" CA  THR E  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.79   -9.25 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   ASN C  60 "
        pdb=" N   THR C  61 "
        pdb=" CA  THR C  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.79   -9.25 1.91e+00 2.74e-01 2.34e+01
  angle pdb=" C   ASN A  60 "
        pdb=" N   THR A  61 "
        pdb=" CA  THR A  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.77   -9.23 1.91e+00 2.74e-01 2.34e+01
  angle pdb=" C   ASN D  60 "
        pdb=" N   THR D  61 "
        pdb=" CA  THR D  61 "
      ideal   model   delta    sigma   weight residual
     121.54  130.75   -9.21 1.91e+00 2.74e-01 2.33e+01
  ... (remaining 17540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 6751
       17.83 -    35.65: 644
       35.65 -    53.48: 120
       53.48 -    71.31: 10
       71.31 -    89.13: 5
  Dihedral angle restraints: 7530
    sinusoidal: 3025
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  LEU B 118 "
           pdb=" C   LEU B 118 "
           pdb=" N   PHE B 119 "
           pdb=" CA  PHE B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  LEU D 118 "
           pdb=" C   LEU D 118 "
           pdb=" N   PHE D 119 "
           pdb=" CA  PHE D 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+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 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1293
       0.043 -    0.087: 396
       0.087 -    0.130: 186
       0.130 -    0.174: 59
       0.174 -    0.217: 16
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CB  ILE A  39 "
            pdb=" CA  ILE A  39 "
            pdb=" CG1 ILE A  39 "
            pdb=" CG2 ILE A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  ILE D  39 "
            pdb=" CA  ILE D  39 "
            pdb=" CG1 ILE D  39 "
            pdb=" CG2 ILE D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE E  39 "
            pdb=" CA  ILE E  39 "
            pdb=" CG1 ILE E  39 "
            pdb=" CG2 ILE E  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 176 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.47e+00
        pdb=" CG  ASP D 176 "   -0.040 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 176 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 176 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 176 "   -0.011 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" CG  ASP A 176 "    0.040 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 176 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 176 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 176 "   -0.011 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" CG  ASP B 176 "    0.040 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 176 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 176 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 4129
        2.85 -     3.36: 10943
        3.36 -     3.87: 21234
        3.87 -     4.39: 24673
        4.39 -     4.90: 42404
  Nonbonded interactions: 103383
  Sorted by model distance:
  nonbonded pdb=" O   SER C 221 "
            pdb=" OG  SER C 221 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   SER B 221 "
            pdb=" OG  SER B 221 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   SER E 221 "
            pdb=" OG  SER E 221 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   SER D 221 "
            pdb=" OG  SER D 221 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   SER A 221 "
            pdb=" OG  SER A 221 "
     model   vdw
     2.335 3.040
  ... (remaining 103378 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'D'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'A'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             1.450
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     10.880
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
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      :  0.005   0.050  12880  Z= 0.210
  Angle     :  0.770   9.307  17545  Z= 0.417
  Chirality :  0.056   0.217   1950
  Planarity :  0.005   0.046   2235
  Dihedral  : 14.077  89.134   4620
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.22), residues: 1525
  helix:  0.24 (0.23), residues: 500
  sheet:  1.44 (0.25), residues: 460
  loop : -3.01 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 299 
 TYR   0.022   0.002   TYR D 248 
 PHE   0.028   0.002   PHE C 116 
 TRP   0.025   0.002   TRP A 206 
 HIS   0.002   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (12880)
  covalent geometry    : angle       0.77038 (17545)
  hydrogen bonds       : bond        0.10650 (  530)
  hydrogen bonds       : angle       5.50754 ( 1545)

*********************** 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
  162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.495 
Fit side-chains
REVERT: B  176 ASP cc_start: 0.7075 (t0) cc_final: 0.6855 (t0)
REVERT: A  158 ASP cc_start: 0.6033 (p0) cc_final: 0.5282 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1172
  time to fit residues: 27.2962
Evaluate side-chains
  145 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
D 298 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.154092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.120757 restraints weight = 13889.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.61
r_work: 0.3103 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12880  Z= 0.127
  Angle     :  0.551   7.674  17545  Z= 0.281
  Chirality :  0.045   0.129   1950
  Planarity :  0.003   0.034   2235
  Dihedral  :  4.782  50.139   1690
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  6.76 %
    Favored  : 93.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.23), residues: 1525
  helix:  1.04 (0.24), residues: 505
  sheet:  1.75 (0.27), residues: 430
  loop : -2.85 (0.23), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 231 
 TYR   0.015   0.001   TYR C 248 
 PHE   0.018   0.001   PHE C 116 
 TRP   0.020   0.001   TRP D 206 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12880)
  covalent geometry    : angle       0.55057 (17545)
  hydrogen bonds       : bond        0.03574 (  530)
  hydrogen bonds       : angle       4.74046 ( 1545)

*********************** 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
  155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.521 
Fit side-chains
REVERT: D   13 ASP cc_start: 0.8289 (m-30) cc_final: 0.8086 (m-30)
REVERT: D  158 ASP cc_start: 0.5985 (p0) cc_final: 0.5738 (p0)
REVERT: B  176 ASP cc_start: 0.7662 (t0) cc_final: 0.7206 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 154
  average time/residue: 0.0955
  time to fit residues: 22.8690
Evaluate side-chains
  133 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 99 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 147 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0270
   chunk 25 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 54 optimal weight:    0.4980
   overall best weight:    1.4842

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.153183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.120250 restraints weight = 14002.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.60
r_work: 0.3125 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12880  Z= 0.125
  Angle     :  0.531   7.678  17545  Z= 0.270
  Chirality :  0.045   0.133   1950
  Planarity :  0.003   0.030   2235
  Dihedral  :  4.499  38.727   1690
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.89 %
    Favored  : 89.53 %
  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 aren not related in a simple way.
  whole:  0.00 (0.23), residues: 1525
  helix:  1.23 (0.24), residues: 515
  sheet:  1.77 (0.27), residues: 430
  loop : -2.72 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 299 
 TYR   0.014   0.001   TYR A 248 
 PHE   0.013   0.001   PHE B 116 
 TRP   0.020   0.001   TRP D 206 
 HIS   0.002   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (12880)
  covalent geometry    : angle       0.53113 (17545)
  hydrogen bonds       : bond        0.03451 (  530)
  hydrogen bonds       : angle       4.57059 ( 1545)

*********************** 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
  155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 147
  time to evaluate  : 0.571 
Fit side-chains
REVERT: D  151 ASN cc_start: 0.7783 (m110) cc_final: 0.7411 (m-40)
REVERT: D  176 ASP cc_start: 0.7609 (t0) cc_final: 0.7208 (t0)
REVERT: C  158 ASP cc_start: 0.6128 (p0) cc_final: 0.5920 (p0)
REVERT: B  265 MET cc_start: 0.8348 (ttm) cc_final: 0.8096 (ttt)
REVERT: A  115 ASP cc_start: 0.7183 (t0) cc_final: 0.6783 (t70)
  outliers start: 8
  outliers final: 3
  residues processed: 152
  average time/residue: 0.0991
  time to fit residues: 23.4421
Evaluate side-chains
  137 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  277 ILE
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain A residue   54 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 143 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 147 optimal weight:   10.0000
   chunk 117 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 144 optimal weight:    0.0870
   chunk 48 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 133 optimal weight:    4.9990
   overall best weight:    2.3764

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.150723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.117807 restraints weight = 13948.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.58
r_work: 0.3087 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12880  Z= 0.165
  Angle     :  0.576   8.786  17545  Z= 0.294
  Chirality :  0.047   0.153   1950
  Planarity :  0.003   0.031   2235
  Dihedral  :  4.662  35.310   1690
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 12.51 %
    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 aren not related in a simple way.
  whole: -0.03 (0.23), residues: 1525
  helix:  1.28 (0.24), residues: 515
  sheet:  1.64 (0.26), residues: 430
  loop : -2.72 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 105 
 TYR   0.017   0.002   TYR A 248 
 PHE   0.014   0.001   PHE C 116 
 TRP   0.018   0.002   TRP D 206 
 HIS   0.003   0.001   HIS D 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (12880)
  covalent geometry    : angle       0.57586 (17545)
  hydrogen bonds       : bond        0.03736 (  530)
  hydrogen bonds       : angle       4.70980 ( 1545)

*********************** 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
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.479 
Fit side-chains
REVERT: E  163 ARG cc_start: 0.7088 (mmt180) cc_final: 0.6790 (mmt180)
REVERT: D  151 ASN cc_start: 0.7786 (m110) cc_final: 0.7439 (m-40)
REVERT: B  151 ASN cc_start: 0.7883 (m110) cc_final: 0.7615 (m110)
REVERT: B  265 MET cc_start: 0.8362 (ttm) cc_final: 0.8139 (ttt)
REVERT: A  151 ASN cc_start: 0.7915 (m110) cc_final: 0.7528 (m-40)
  outliers start: 17
  outliers final: 12
  residues processed: 167
  average time/residue: 0.0968
  time to fit residues: 24.2711
Evaluate side-chains
  156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  277 ILE
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 135 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 90 optimal weight:   10.0000
   chunk 139 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
E 284 HIS
D 151 ASN
D 284 HIS
C 284 HIS
B 284 HIS
A 284 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.147197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.114305 restraints weight = 14095.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.58
r_work: 0.3042 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  12880  Z= 0.269
  Angle     :  0.698  10.022  17545  Z= 0.357
  Chirality :  0.052   0.184   1950
  Planarity :  0.004   0.033   2235
  Dihedral  :  5.227  44.702   1690
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.51 %
    Favored  : 82.04 %
  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 aren not related in a simple way.
  whole: -0.43 (0.22), residues: 1525
  helix:  1.00 (0.24), residues: 505
  sheet:  1.35 (0.26), residues: 430
  loop : -2.86 (0.24), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  65 
 TYR   0.024   0.002   TYR C 248 
 PHE   0.017   0.002   PHE B 116 
 TRP   0.020   0.002   TRP B 206 
 HIS   0.004   0.001   HIS E 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00637 (12880)
  covalent geometry    : angle       0.69849 (17545)
  hydrogen bonds       : bond        0.04588 (  530)
  hydrogen bonds       : angle       5.09212 ( 1545)

*********************** 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
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.304 
Fit side-chains
REVERT: E   31 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7451 (mp10)
REVERT: E  161 TRP cc_start: 0.7768 (m-10) cc_final: 0.7519 (m-10)
REVERT: E  163 ARG cc_start: 0.6995 (mmt180) cc_final: 0.6744 (mmt180)
REVERT: D  151 ASN cc_start: 0.7892 (m-40) cc_final: 0.7633 (m-40)
REVERT: D  230 GLU cc_start: 0.5446 (mt-10) cc_final: 0.4705 (mm-30)
REVERT: C  163 ARG cc_start: 0.7014 (mmt180) cc_final: 0.6733 (mmt180)
REVERT: B  151 ASN cc_start: 0.7910 (m110) cc_final: 0.7664 (m110)
REVERT: B  163 ARG cc_start: 0.7064 (mmt180) cc_final: 0.6816 (mmt180)
REVERT: B  265 MET cc_start: 0.8374 (ttm) cc_final: 0.8110 (ttt)
REVERT: A   31 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7279 (mt0)
REVERT: A  151 ASN cc_start: 0.7939 (m110) cc_final: 0.7610 (m-40)
REVERT: A  163 ARG cc_start: 0.7111 (mmt180) cc_final: 0.6842 (mmt180)
  outliers start: 20
  outliers final: 17
  residues processed: 164
  average time/residue: 0.1167
  time to fit residues: 26.8648
Evaluate side-chains
  160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 GLN
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain D residue  277 ILE
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  234 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 120 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 121 optimal weight:    0.0670
   chunk 5 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    1.5722

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.158149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.129964 restraints weight = 13827.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.30
r_work: 0.3134 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12880  Z= 0.133
  Angle     :  0.545   8.063  17545  Z= 0.278
  Chirality :  0.046   0.131   1950
  Planarity :  0.003   0.034   2235
  Dihedral  :  4.635  35.949   1690
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 17.53 %
    Favored  : 80.95 %
  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 aren not related in a simple way.
  whole: -0.13 (0.23), residues: 1525
  helix:  1.21 (0.24), residues: 515
  sheet:  1.47 (0.26), residues: 430
  loop : -2.68 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 117 
 TYR   0.013   0.001   TYR A 248 
 PHE   0.013   0.001   PHE B 116 
 TRP   0.020   0.001   TRP B 206 
 HIS   0.003   0.001   HIS C 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (12880)
  covalent geometry    : angle       0.54474 (17545)
  hydrogen bonds       : bond        0.03507 (  530)
  hydrogen bonds       : angle       4.69894 ( 1545)

*********************** 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
  168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.377 
Fit side-chains
REVERT: E  163 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6775 (mmt180)
REVERT: D  151 ASN cc_start: 0.7781 (m-40) cc_final: 0.7506 (m-40)
REVERT: C  163 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6757 (mmt180)
REVERT: C  174 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7457 (mtp180)
REVERT: C  233 GLN cc_start: 0.6971 (tp40) cc_final: 0.6571 (mt0)
REVERT: B  151 ASN cc_start: 0.7830 (m110) cc_final: 0.7593 (m110)
REVERT: B  163 ARG cc_start: 0.7085 (mmt180) cc_final: 0.6843 (mmt180)
REVERT: A  163 ARG cc_start: 0.7092 (mmt180) cc_final: 0.6863 (mmt180)
  outliers start: 21
  outliers final: 18
  residues processed: 165
  average time/residue: 0.0985
  time to fit residues: 23.9125
Evaluate side-chains
  157 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  261 VAL
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 117 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 120 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.148066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.116626 restraints weight = 13952.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.47
r_work: 0.3072 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12880  Z= 0.210
  Angle     :  0.630   9.274  17545  Z= 0.322
  Chirality :  0.049   0.167   1950
  Planarity :  0.003   0.035   2235
  Dihedral  :  4.922  38.609   1690
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.18 %
    Favored  : 79.71 %
  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 aren not related in a simple way.
  whole: -0.31 (0.23), residues: 1525
  helix:  1.11 (0.24), residues: 510
  sheet:  1.24 (0.26), residues: 435
  loop : -2.71 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 231 
 TYR   0.018   0.002   TYR E 248 
 PHE   0.015   0.002   PHE C 116 
 TRP   0.021   0.002   TRP D 206 
 HIS   0.002   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (12880)
  covalent geometry    : angle       0.63006 (17545)
  hydrogen bonds       : bond        0.04090 (  530)
  hydrogen bonds       : angle       4.89776 ( 1545)

*********************** 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
  181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 0.491 
Fit side-chains
REVERT: E   31 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7503 (mp10)
REVERT: E  163 ARG cc_start: 0.6985 (mmt180) cc_final: 0.6762 (mmt180)
REVERT: D   31 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6861 (mt0)
REVERT: D  117 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.5847 (mtt180)
REVERT: D  151 ASN cc_start: 0.7885 (m-40) cc_final: 0.7581 (m-40)
REVERT: C   31 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7295 (mt0)
REVERT: C  117 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.5771 (mtt180)
REVERT: C  163 ARG cc_start: 0.7035 (mmt180) cc_final: 0.6779 (mmt180)
REVERT: C  233 GLN cc_start: 0.7020 (tp40) cc_final: 0.6591 (mt0)
REVERT: B  117 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5889 (mtt180)
REVERT: B  151 ASN cc_start: 0.7897 (m110) cc_final: 0.7659 (m110)
REVERT: B  163 ARG cc_start: 0.7044 (mmt180) cc_final: 0.6820 (mmt180)
REVERT: B  233 GLN cc_start: 0.6913 (tp40) cc_final: 0.6484 (mt0)
REVERT: A   31 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7302 (mt0)
REVERT: A  117 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.5885 (mtt180)
REVERT: A  151 ASN cc_start: 0.7934 (m110) cc_final: 0.7585 (m-40)
REVERT: A  163 ARG cc_start: 0.7112 (mmt180) cc_final: 0.6867 (mmt180)
  outliers start: 29
  outliers final: 17
  residues processed: 176
  average time/residue: 0.1217
  time to fit residues: 30.2567
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 GLN
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain D residue   31 GLN
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
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:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0770
   chunk 139 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 55 optimal weight:    0.8980
   chunk 96 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    1.7942

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.150328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.117915 restraints weight = 13875.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.56
r_work: 0.3090 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12880  Z= 0.139
  Angle     :  0.553   8.110  17545  Z= 0.282
  Chirality :  0.046   0.135   1950
  Planarity :  0.003   0.034   2235
  Dihedral  :  4.631  33.029   1690
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.18 %
    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 aren not related in a simple way.
  whole: -0.15 (0.23), residues: 1525
  helix:  1.23 (0.24), residues: 515
  sheet:  1.34 (0.26), residues: 435
  loop : -2.65 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 117 
 TYR   0.014   0.001   TYR A 248 
 PHE   0.014   0.001   PHE D 236 
 TRP   0.021   0.002   TRP B 206 
 HIS   0.002   0.001   HIS C 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12880)
  covalent geometry    : angle       0.55345 (17545)
  hydrogen bonds       : bond        0.03528 (  530)
  hydrogen bonds       : angle       4.69844 ( 1545)

*********************** 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
  178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.515 
Fit side-chains
REVERT: E   49 LYS cc_start: 0.6970 (tppt) cc_final: 0.5845 (tptt)
REVERT: E  163 ARG cc_start: 0.6977 (mmt180) cc_final: 0.6752 (mmt180)
REVERT: D  117 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5727 (mtt180)
REVERT: D  151 ASN cc_start: 0.7780 (m-40) cc_final: 0.7506 (m-40)
REVERT: C   31 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7307 (mt0)
REVERT: C   59 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8214 (mm-30)
REVERT: C  117 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.5638 (mtt180)
REVERT: C  163 ARG cc_start: 0.7007 (mmt180) cc_final: 0.6738 (mmt180)
REVERT: C  233 GLN cc_start: 0.6968 (tp40) cc_final: 0.6478 (mt0)
REVERT: C  245 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.6298 (t80)
REVERT: B  117 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5701 (mtt180)
REVERT: B  151 ASN cc_start: 0.7865 (m110) cc_final: 0.7645 (m110)
REVERT: B  163 ARG cc_start: 0.6983 (mmt180) cc_final: 0.6753 (mmt180)
REVERT: B  233 GLN cc_start: 0.6884 (tp40) cc_final: 0.6438 (mt0)
REVERT: B  245 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6278 (t80)
REVERT: A  117 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.5755 (mtt180)
REVERT: A  163 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6895 (mmt180)
  outliers start: 30
  outliers final: 20
  residues processed: 175
  average time/residue: 0.1175
  time to fit residues: 28.8790
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  277 ILE
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:    8.9990
   chunk 122 optimal weight:    1.9990
   chunk 105 optimal weight:   10.0000
   chunk 136 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.148974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.117578 restraints weight = 14048.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.47
r_work: 0.3081 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12880  Z= 0.183
  Angle     :  0.601   8.860  17545  Z= 0.307
  Chirality :  0.048   0.154   1950
  Planarity :  0.003   0.035   2235
  Dihedral  :  4.792  34.710   1690
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.96 %
    Favored  : 79.56 %
  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 aren not related in a simple way.
  whole: -0.24 (0.23), residues: 1525
  helix:  1.16 (0.24), residues: 515
  sheet:  1.26 (0.26), residues: 435
  loop : -2.68 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  65 
 TYR   0.016   0.002   TYR C 248 
 PHE   0.015   0.002   PHE D 116 
 TRP   0.021   0.002   TRP D 206 
 HIS   0.002   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (12880)
  covalent geometry    : angle       0.60145 (17545)
  hydrogen bonds       : bond        0.03869 (  530)
  hydrogen bonds       : angle       4.81019 ( 1545)

*********************** 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
  182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 0.513 
Fit side-chains
REVERT: E  163 ARG cc_start: 0.6984 (mmt180) cc_final: 0.6773 (mmt180)
REVERT: E  245 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.5599 (t80)
REVERT: D  117 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.5851 (mtt180)
REVERT: D  151 ASN cc_start: 0.7850 (m-40) cc_final: 0.7536 (m-40)
REVERT: D  245 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.5848 (t80)
REVERT: C   31 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7312 (mt0)
REVERT: C  117 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.5752 (mtt180)
REVERT: C  174 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7516 (mtp180)
REVERT: C  233 GLN cc_start: 0.6996 (tp40) cc_final: 0.6561 (mt0)
REVERT: B  117 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.5796 (mtt180)
REVERT: B  151 ASN cc_start: 0.7905 (m110) cc_final: 0.7661 (m110)
REVERT: B  163 ARG cc_start: 0.6999 (mmt180) cc_final: 0.6763 (mmt180)
REVERT: B  233 GLN cc_start: 0.6884 (tp40) cc_final: 0.6464 (mt0)
REVERT: B  245 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6288 (t80)
REVERT: A   31 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7270 (mt0)
REVERT: A  117 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.5845 (mtt180)
REVERT: A  163 ARG cc_start: 0.7155 (mmt180) cc_final: 0.6923 (mmt180)
REVERT: A  245 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.5549 (t80)
  outliers start: 34
  outliers final: 15
  residues processed: 176
  average time/residue: 0.1371
  time to fit residues: 33.6975
Evaluate side-chains
  171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain D residue  277 ILE
Chi-restraints excluded: chain C residue   31 GLN
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 119 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 112 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0770
   chunk 51 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9544

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.152319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.120057 restraints weight = 13963.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.56
r_work: 0.3122 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12880  Z= 0.109
  Angle     :  0.520   6.974  17545  Z= 0.264
  Chirality :  0.045   0.143   1950
  Planarity :  0.003   0.035   2235
  Dihedral  :  4.307  24.736   1690
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.76 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.23), residues: 1525
  helix:  1.41 (0.24), residues: 515
  sheet:  1.49 (0.26), residues: 435
  loop : -2.56 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 174 
 TYR   0.010   0.001   TYR A 248 
 PHE   0.015   0.001   PHE C 236 
 TRP   0.020   0.001   TRP D 206 
 HIS   0.002   0.001   HIS C 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (12880)
  covalent geometry    : angle       0.51951 (17545)
  hydrogen bonds       : bond        0.03186 (  530)
  hydrogen bonds       : angle       4.52882 ( 1545)

********************** 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
  167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.514 
Fit side-chains
REVERT: E   49 LYS cc_start: 0.6985 (tppt) cc_final: 0.5863 (tptt)
REVERT: E  163 ARG cc_start: 0.6974 (mmt180) cc_final: 0.6741 (mmt180)
REVERT: E  245 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.5640 (t80)
REVERT: D  113 ASP cc_start: 0.7500 (m-30) cc_final: 0.6930 (p0)
REVERT: D  117 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6493 (mpt180)
REVERT: D  151 ASN cc_start: 0.7714 (m-40) cc_final: 0.7453 (m-40)
REVERT: D  245 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.5774 (t80)
REVERT: C   49 LYS cc_start: 0.6913 (tppt) cc_final: 0.5835 (tptt)
REVERT: C  117 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6116 (mpt180)
REVERT: C  174 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7505 (mtp180)
REVERT: C  233 GLN cc_start: 0.6939 (tp40) cc_final: 0.6464 (mt0)
REVERT: C  245 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6383 (t80)
REVERT: B  117 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.5538 (mtt180)
REVERT: B  151 ASN cc_start: 0.7824 (m110) cc_final: 0.7598 (m110)
REVERT: B  163 ARG cc_start: 0.6964 (mmt180) cc_final: 0.6729 (mmt180)
REVERT: B  233 GLN cc_start: 0.6854 (tp40) cc_final: 0.6370 (mt0)
REVERT: B  245 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6447 (t80)
REVERT: A  113 ASP cc_start: 0.7448 (m-30) cc_final: 0.6967 (p0)
REVERT: A  117 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6416 (mpt180)
REVERT: A  163 ARG cc_start: 0.7127 (mmt180) cc_final: 0.6882 (mmt180)
REVERT: A  245 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.5707 (t80)
  outliers start: 25
  outliers final: 12
  residues processed: 165
  average time/residue: 0.1390
  time to fit residues: 32.0767
Evaluate side-chains
  160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   39 ILE
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  245 TYR
Chi-restraints excluded: chain D residue  117 ARG
Chi-restraints excluded: chain D residue  168 THR
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain D residue  245 TYR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  117 ARG
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  117 ARG
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 124 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 141 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
E 151 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.150761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.118388 restraints weight = 13944.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.56
r_work: 0.3098 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12880  Z= 0.137
  Angle     :  0.554   7.945  17545  Z= 0.281
  Chirality :  0.046   0.137   1950
  Planarity :  0.003   0.035   2235
  Dihedral  :  4.434  27.377   1690
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.84 %
    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 aren not related in a simple way.
  whole:  0.06 (0.23), residues: 1525
  helix:  1.37 (0.24), residues: 515
  sheet:  1.50 (0.26), residues: 435
  loop : -2.55 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 231 
 TYR   0.013   0.001   TYR A 248 
 PHE   0.013   0.001   PHE C 116 
 TRP   0.022   0.002   TRP D 206 
 HIS   0.002   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12880)
  covalent geometry    : angle       0.55369 (17545)
  hydrogen bonds       : bond        0.03466 (  530)
  hydrogen bonds       : angle       4.59600 ( 1545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3020.20 seconds
wall clock time: 52 minutes 21.62 seconds (3141.62 seconds total)