Starting phenix.real_space_refine
on Tue Mar  3 18:33:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vx3_21428/03_2026/6vx3_21428_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vx3_21428/03_2026/6vx3_21428.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2026/6vx3_21428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2026/6vx3_21428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2026/6vx3_21428_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2026/6vx3_21428_neut.cif"
  }
  resolution = 3.7
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      24      5.16       5
     C    5336      2.51       5
     N    1188      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7780
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 1841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1841
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 7, 'TRANS': 217}
    Chain: "C"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 104
          Unusual residues: {'POV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    A, B, D
  Time building chain proxies: 1.42, per 1000 atoms: 0.18
  Number of scatterers: 7780
  At special positions: 0
  Unit cell: (125.882, 125.882, 65.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P       8     15.00
     O    1224      8.00
     N    1188      7.00
     C    5336      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 292.5 milliseconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      74.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'C' and resid 24 through 43
      removed outlier: 3.554A  pdb=" N   ILE C  42 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 52
    Processing helix  chain 'C' and resid 52 through 76
      removed outlier: 4.310A  pdb=" N   ARG C  58 " --> pdb=" O   TRP C  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE C  69 " --> pdb=" O   TRP C  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU C  70 " --> pdb=" O   ILE C  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG C  74 " --> pdb=" O   GLU C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 103
    Processing helix  chain 'C' and resid 104 through 106
      No H-bonds generated for 'chain 'C' and resid 104 through 106'
    Processing helix  chain 'C' and resid 110 through 119
      removed outlier: 3.672A  pdb=" N   ILE C 114 " --> pdb=" O   THR C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 125
    Processing helix  chain 'C' and resid 130 through 140
    Processing helix  chain 'C' and resid 146 through 166
      removed outlier: 3.860A  pdb=" N   PHE C 155 " --> pdb=" O   MET C 151 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   PHE C 158 " --> pdb=" O   PHE C 154 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR C 163 " --> pdb=" O   ALA C 159 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   MET C 164 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU C 165 " --> pdb=" O   ILE C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 175
    Processing helix  chain 'C' and resid 178 through 187
      removed outlier: 4.181A  pdb=" N   LEU C 182 " --> pdb=" O   GLN C 178 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR C 183 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE C 201 " --> pdb=" O   VAL C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 207
      No H-bonds generated for 'chain 'C' and resid 205 through 207'
    Processing helix  chain 'C' and resid 208 through 213
      removed outlier: 3.760A  pdb=" N   PHE C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 237
      removed outlier: 3.576A  pdb=" N   PHE C 227 " --> pdb=" O   ILE C 223 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASN C 233 " --> pdb=" O   GLY C 229 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN C 234 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C 235 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS C 237 " --> pdb=" O   ASN C 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 43
      removed outlier: 3.554A  pdb=" N   ILE A  42 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 52 through 76
      removed outlier: 4.311A  pdb=" N   ARG A  58 " --> pdb=" O   TRP A  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU A  70 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 103
    Processing helix  chain 'A' and resid 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 110 through 119
      removed outlier: 3.672A  pdb=" N   ILE A 114 " --> pdb=" O   THR A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 125
    Processing helix  chain 'A' and resid 130 through 140
    Processing helix  chain 'A' and resid 146 through 166
      removed outlier: 3.860A  pdb=" N   PHE A 155 " --> pdb=" O   MET A 151 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   PHE A 158 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   MET A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 178 through 187
      removed outlier: 4.182A  pdb=" N   LEU A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.760A  pdb=" N   PHE A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 237
      removed outlier: 3.576A  pdb=" N   PHE A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN A 233 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASN A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 43
      removed outlier: 3.553A  pdb=" N   ILE B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 52
    Processing helix  chain 'B' and resid 52 through 76
      removed outlier: 4.310A  pdb=" N   ARG B  58 " --> pdb=" O   TRP B  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE B  69 " --> pdb=" O   TRP B  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU B  70 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 103
    Processing helix  chain 'B' and resid 104 through 106
      No H-bonds generated for 'chain 'B' and resid 104 through 106'
    Processing helix  chain 'B' and resid 110 through 119
      removed outlier: 3.671A  pdb=" N   ILE B 114 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 125
    Processing helix  chain 'B' and resid 130 through 140
    Processing helix  chain 'B' and resid 146 through 166
      removed outlier: 3.861A  pdb=" N   PHE B 155 " --> pdb=" O   MET B 151 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE B 158 " --> pdb=" O   PHE B 154 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR B 163 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   MET B 164 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B 165 " --> pdb=" O   ILE B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 175
    Processing helix  chain 'B' and resid 178 through 187
      removed outlier: 4.182A  pdb=" N   LEU B 182 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 207
      No H-bonds generated for 'chain 'B' and resid 205 through 207'
    Processing helix  chain 'B' and resid 208 through 213
      removed outlier: 3.761A  pdb=" N   PHE B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.577A  pdb=" N   PHE B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN B 233 " --> pdb=" O   GLY B 229 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B 234 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 235 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS B 237 " --> pdb=" O   ASN B 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 43
      removed outlier: 3.553A  pdb=" N   ILE D  42 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 52
    Processing helix  chain 'D' and resid 52 through 76
      removed outlier: 4.310A  pdb=" N   ARG D  58 " --> pdb=" O   TRP D  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE D  69 " --> pdb=" O   TRP D  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU D  70 " --> pdb=" O   ILE D  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG D  74 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 103
    Processing helix  chain 'D' and resid 104 through 106
      No H-bonds generated for 'chain 'D' and resid 104 through 106'
    Processing helix  chain 'D' and resid 110 through 119
      removed outlier: 3.672A  pdb=" N   ILE D 114 " --> pdb=" O   THR D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 125
    Processing helix  chain 'D' and resid 130 through 140
    Processing helix  chain 'D' and resid 146 through 166
      removed outlier: 3.860A  pdb=" N   PHE D 155 " --> pdb=" O   MET D 151 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE D 158 " --> pdb=" O   PHE D 154 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   MET D 164 " --> pdb=" O   VAL D 160 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU D 165 " --> pdb=" O   ILE D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 175
    Processing helix  chain 'D' and resid 178 through 187
      removed outlier: 4.181A  pdb=" N   LEU D 182 " --> pdb=" O   GLN D 178 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR D 183 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE D 201 " --> pdb=" O   VAL D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 207
      No H-bonds generated for 'chain 'D' and resid 205 through 207'
    Processing helix  chain 'D' and resid 208 through 213
      removed outlier: 3.760A  pdb=" N   PHE D 212 " --> pdb=" O   SER D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 237
      removed outlier: 3.577A  pdb=" N   PHE D 227 " --> pdb=" O   ILE D 223 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASN D 233 " --> pdb=" O   GLY D 229 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN D 234 " --> pdb=" O   VAL D 230 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL D 235 " --> pdb=" O   ILE D 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS D 237 " --> pdb=" O   ASN D 233 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1032 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: 1.07

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1914
        1.33 -     1.45: 1531
        1.45 -     1.57: 4479
        1.57 -     1.69: 16
        1.69 -     1.80: 48
  Bond restraints: 7988
  Sorted by residual:
  bond pdb=" C31 POV A 301 "
       pdb=" O31 POV A 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.454 -0.127 2.00e-02 2.50e+03 4.02e+01
  bond pdb=" C31 POV C 301 "
       pdb=" O31 POV C 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.453 -0.126 2.00e-02 2.50e+03 3.99e+01
  bond pdb=" C31 POV B 301 "
       pdb=" O31 POV B 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.453 -0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C31 POV D 301 "
       pdb=" O31 POV D 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.453 -0.126 2.00e-02 2.50e+03 3.97e+01
  bond pdb=" C31 POV A 302 "
       pdb=" O31 POV A 302 "
    ideal  model  delta    sigma   weight residual
    1.327  1.451 -0.124 2.00e-02 2.50e+03 3.81e+01
  ... (remaining 7983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 10241
        2.05 -     4.11: 395
        4.11 -     6.16: 104
        6.16 -     8.21: 44
        8.21 -    10.26: 20
  Bond angle restraints: 10804
  Sorted by residual:
  angle pdb=" C   PHE D  67 "
        pdb=" N   THR D  68 "
        pdb=" CA  THR D  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.73   -6.91 1.50e+00 4.44e-01 2.12e+01
  angle pdb=" C   PHE A  67 "
        pdb=" N   THR A  68 "
        pdb=" CA  THR A  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.70   -6.88 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" C   PHE C  67 "
        pdb=" N   THR C  68 "
        pdb=" CA  THR C  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.69   -6.87 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" N   ILE D  59 "
        pdb=" CA  ILE D  59 "
        pdb=" C   ILE D  59 "
      ideal   model   delta    sigma   weight residual
     110.72  115.33   -4.61 1.01e+00 9.80e-01 2.08e+01
  angle pdb=" C   PHE B  67 "
        pdb=" N   THR B  68 "
        pdb=" CA  THR B  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.66   -6.84 1.50e+00 4.44e-01 2.08e+01
  ... (remaining 10799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.06: 4112
       22.06 -    44.12: 436
       44.12 -    66.18: 84
       66.18 -    88.23: 28
       88.23 -   110.29: 8
  Dihedral angle restraints: 4668
    sinusoidal: 2020
      harmonic: 2648
  Sorted by residual:
  dihedral pdb=" C29 POV C 301 "
           pdb="C210 POV C 301 "
           pdb="C211 POV C 301 "
           pdb="C212 POV C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -137.46 -110.29     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" C29 POV A 301 "
           pdb="C210 POV A 301 "
           pdb="C211 POV A 301 "
           pdb="C212 POV A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -137.46 -110.29     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" C29 POV D 301 "
           pdb="C210 POV D 301 "
           pdb="C211 POV D 301 "
           pdb="C212 POV D 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -137.47 -110.28     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 4665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 691
       0.036 -    0.072: 381
       0.072 -    0.108: 127
       0.108 -    0.145: 21
       0.145 -    0.181: 12
  Chirality restraints: 1232
  Sorted by residual:
  chirality pdb=" CA  LEU A 177 "
            pdb=" N   LEU A 177 "
            pdb=" C   LEU A 177 "
            pdb=" CB  LEU A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CA  LEU C 177 "
            pdb=" N   LEU C 177 "
            pdb=" C   LEU C 177 "
            pdb=" CB  LEU C 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  LEU B 177 "
            pdb=" N   LEU B 177 "
            pdb=" C   LEU B 177 "
            pdb=" CB  LEU B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.95e-01
  ... (remaining 1229 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  64 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.73e+00
        pdb=" C   LEU B  64 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   LEU B  64 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TRP B  65 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D  64 "    0.015 2.00e-02 2.50e+03   2.94e-02 8.66e+00
        pdb=" C   LEU D  64 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   LEU D  64 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TRP D  65 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  64 "   -0.015 2.00e-02 2.50e+03   2.94e-02 8.64e+00
        pdb=" C   LEU C  64 "    0.051 2.00e-02 2.50e+03
        pdb=" O   LEU C  64 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TRP C  65 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 48
        2.44 -     3.06: 5553
        3.06 -     3.67: 10767
        3.67 -     4.29: 15929
        4.29 -     4.90: 26155
  Nonbonded interactions: 58452
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  60 "
            pdb=" NH2 ARG D 116 "
     model   vdw
     1.829 3.120
  nonbonded pdb=" OD2 ASP A  60 "
            pdb=" NH2 ARG A 116 "
     model   vdw
     1.829 3.120
  nonbonded pdb=" OD2 ASP C  60 "
            pdb=" NH2 ARG C 116 "
     model   vdw
     1.829 3.120
  nonbonded pdb=" OD2 ASP B  60 "
            pdb=" NH2 ARG B 116 "
     model   vdw
     1.830 3.120
  nonbonded pdb=" O   GLN D 178 "
            pdb=" O32 POV D 302 "
     model   vdw
     2.014 3.040
  ... (remaining 58447 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.270
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
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      :  0.009   0.127   7992  Z= 0.430
  Angle     :  1.110  10.264  10804  Z= 0.573
  Chirality :  0.049   0.181   1232
  Planarity :  0.004   0.030   1256
  Dihedral  : 19.669 110.293   2940
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 26.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 10.55 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.21 (0.24), residues: 892
  helix: -2.22 (0.18), residues: 580
  sheet:  None (None), residues: 0
  loop : -3.72 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  74 
 TYR   0.008   0.001   TYR C 173 
 PHE   0.023   0.002   PHE D 155 
 TRP   0.009   0.001   TRP C  91 
 HIS   0.003   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00892 ( 7988)
  covalent geometry    : angle       1.10984 (10804)
  hydrogen bonds       : bond        0.20078 (  356)
  hydrogen bonds       : angle       7.97601 ( 1032)
  Misc. bond           : bond        0.00333 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 200
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   48 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8310 (mm)
REVERT: C   57 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5184 (t80)
REVERT: C  191 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: C  224 PHE cc_start: 0.7177 (t80) cc_final: 0.6607 (t80)
REVERT: C  234 ASN cc_start: 0.8423 (t0) cc_final: 0.8048 (t0)
REVERT: A   48 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8334 (mm)
REVERT: A   57 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.5307 (t80)
REVERT: A  191 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8357 (tm-30)
REVERT: A  224 PHE cc_start: 0.7026 (t80) cc_final: 0.6623 (t80)
REVERT: B   48 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8348 (mm)
REVERT: B   57 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5536 (t80)
REVERT: B   63 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8594 (mm)
REVERT: B  191 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: D   48 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8320 (mm)
REVERT: D   57 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5180 (t80)
REVERT: D  191 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: D  224 PHE cc_start: 0.7133 (t80) cc_final: 0.6883 (t80)
  outliers start: 32
  outliers final: 14
  residues processed: 220
  average time/residue: 0.0612
  time to fit residues: 20.6804
Evaluate side-chains
  177 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain D residue   48 ILE
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue   65 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0570
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
C 225 ASN
A  52 HIS
B  52 HIS
B 225 ASN
D  52 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.149239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.113401 restraints weight = 12173.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.116585 restraints weight = 7079.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.118740 restraints weight = 5048.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.120100 restraints weight = 4105.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.120463 restraints weight = 3613.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7992  Z= 0.133
  Angle     :  0.609   8.786  10804  Z= 0.307
  Chirality :  0.041   0.125   1232
  Planarity :  0.003   0.023   1256
  Dihedral  : 20.254 111.740   1358
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 19.10 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.26), residues: 892
  helix: -1.40 (0.19), residues: 636
  sheet:  None (None), residues: 0
  loop : -3.27 (0.34), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 116 
 TYR   0.005   0.001   TYR C 156 
 PHE   0.012   0.001   PHE D 227 
 TRP   0.008   0.001   TRP C  54 
 HIS   0.005   0.002   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7988)
  covalent geometry    : angle       0.60944 (10804)
  hydrogen bonds       : bond        0.04871 (  356)
  hydrogen bonds       : angle       5.34184 ( 1032)
  Misc. bond           : bond        0.00065 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 189
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8832 (t80) cc_final: 0.8544 (t80)
REVERT: C   57 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.5470 (t80)
REVERT: C   65 TRP cc_start: 0.5733 (OUTLIER) cc_final: 0.4270 (t60)
REVERT: C  139 MET cc_start: 0.8045 (tpp) cc_final: 0.7653 (tpp)
REVERT: C  191 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8260 (tm-30)
REVERT: C  201 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8590 (mt)
REVERT: C  224 PHE cc_start: 0.6839 (t80) cc_final: 0.6613 (t80)
REVERT: A   35 PHE cc_start: 0.8836 (t80) cc_final: 0.8481 (t80)
REVERT: A   52 HIS cc_start: 0.6382 (OUTLIER) cc_final: 0.5759 (m-70)
REVERT: A   57 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.5702 (t80)
REVERT: A   65 TRP cc_start: 0.5670 (OUTLIER) cc_final: 0.4280 (t60)
REVERT: A  138 VAL cc_start: 0.9495 (p) cc_final: 0.9190 (m)
REVERT: A  139 MET cc_start: 0.8173 (tpp) cc_final: 0.7609 (tpp)
REVERT: A  191 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: A  201 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8543 (mt)
REVERT: B   35 PHE cc_start: 0.8813 (t80) cc_final: 0.8454 (t80)
REVERT: B   52 HIS cc_start: 0.6454 (OUTLIER) cc_final: 0.5724 (m-70)
REVERT: B   57 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.5485 (t80)
REVERT: B   65 TRP cc_start: 0.5598 (OUTLIER) cc_final: 0.4215 (t60)
REVERT: B  191 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: B  201 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8550 (mt)
REVERT: D   35 PHE cc_start: 0.8809 (t80) cc_final: 0.8474 (t80)
REVERT: D   52 HIS cc_start: 0.6377 (OUTLIER) cc_final: 0.5668 (m-70)
REVERT: D   57 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5478 (t80)
REVERT: D   65 TRP cc_start: 0.5546 (OUTLIER) cc_final: 0.4100 (t60)
REVERT: D  139 MET cc_start: 0.8123 (tpp) cc_final: 0.7762 (tpp)
REVERT: D  191 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: D  201 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8533 (mt)
REVERT: D  224 PHE cc_start: 0.6823 (t80) cc_final: 0.6608 (t80)
  outliers start: 34
  outliers final: 17
  residues processed: 203
  average time/residue: 0.0683
  time to fit residues: 20.3645
Evaluate side-chains
  193 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 161
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  201 ILE
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   52 HIS
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   52 HIS
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   65 TRP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 101 HIS
A 101 HIS
A 225 ASN
B 101 HIS
D 101 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.149190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.112832 restraints weight = 11922.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.115887 restraints weight = 6937.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.117918 restraints weight = 5008.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.119036 restraints weight = 4119.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.119960 restraints weight = 3676.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7992  Z= 0.126
  Angle     :  0.555   6.479  10804  Z= 0.282
  Chirality :  0.040   0.112   1232
  Planarity :  0.003   0.027   1256
  Dihedral  : 18.957 109.476   1328
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 23.24 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.28), residues: 892
  helix: -0.93 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.90 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 122 
 TYR   0.009   0.001   TYR C  49 
 PHE   0.014   0.001   PHE D 227 
 TRP   0.009   0.001   TRP C  54 
 HIS   0.009   0.002   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7988)
  covalent geometry    : angle       0.55498 (10804)
  hydrogen bonds       : bond        0.04319 (  356)
  hydrogen bonds       : angle       4.83717 ( 1032)
  Misc. bond           : bond        0.00052 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 191
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8791 (t80) cc_final: 0.8446 (t80)
REVERT: C   51 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7375 (p0)
REVERT: C   57 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.5624 (t80)
REVERT: C   65 TRP cc_start: 0.5854 (OUTLIER) cc_final: 0.4198 (t60)
REVERT: C  138 VAL cc_start: 0.9466 (p) cc_final: 0.9175 (m)
REVERT: C  139 MET cc_start: 0.8141 (tpp) cc_final: 0.7657 (tpp)
REVERT: C  191 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: C  201 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8640 (mt)
REVERT: A   57 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5629 (t80)
REVERT: A   65 TRP cc_start: 0.5943 (OUTLIER) cc_final: 0.4353 (t60)
REVERT: A  138 VAL cc_start: 0.9459 (p) cc_final: 0.9163 (m)
REVERT: A  139 MET cc_start: 0.8291 (tpp) cc_final: 0.7727 (tpp)
REVERT: A  191 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: A  201 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8640 (mt)
REVERT: B   57 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5589 (t80)
REVERT: B   65 TRP cc_start: 0.5837 (OUTLIER) cc_final: 0.4267 (t60)
REVERT: B  138 VAL cc_start: 0.9426 (p) cc_final: 0.9105 (m)
REVERT: B  139 MET cc_start: 0.8291 (tpp) cc_final: 0.7874 (tpp)
REVERT: B  191 GLU cc_start: 0.8616 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: B  201 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8563 (mt)
REVERT: B  224 PHE cc_start: 0.6251 (t80) cc_final: 0.5615 (t80)
REVERT: D   35 PHE cc_start: 0.8786 (t80) cc_final: 0.8360 (t80)
REVERT: D   57 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5630 (t80)
REVERT: D   65 TRP cc_start: 0.5888 (OUTLIER) cc_final: 0.4222 (t60)
REVERT: D  138 VAL cc_start: 0.9490 (p) cc_final: 0.9186 (m)
REVERT: D  139 MET cc_start: 0.8234 (tpp) cc_final: 0.7783 (tpp)
REVERT: D  191 GLU cc_start: 0.8626 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: D  201 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8609 (mt)
  outliers start: 44
  outliers final: 30
  residues processed: 209
  average time/residue: 0.0788
  time to fit residues: 22.8313
Evaluate side-chains
  220 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  201 ILE
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   65 TRP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0070
   chunk 4 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
C 101 HIS
C 225 ASN
A 101 HIS
A 225 ASN
D 101 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.149456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.114705 restraints weight = 11938.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.117878 restraints weight = 6834.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119982 restraints weight = 4823.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.121179 restraints weight = 3894.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.122009 restraints weight = 3430.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7992  Z= 0.123
  Angle     :  0.537   6.617  10804  Z= 0.272
  Chirality :  0.040   0.111   1232
  Planarity :  0.003   0.027   1256
  Dihedral  : 17.946 102.692   1328
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 23.74 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.28), residues: 892
  helix: -0.66 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.67 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  74 
 TYR   0.015   0.001   TYR C  49 
 PHE   0.015   0.001   PHE D 224 
 TRP   0.008   0.001   TRP A  54 
 HIS   0.001   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7988)
  covalent geometry    : angle       0.53722 (10804)
  hydrogen bonds       : bond        0.03907 (  356)
  hydrogen bonds       : angle       4.60640 ( 1032)
  Misc. bond           : bond        0.00054 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 186
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8777 (t80) cc_final: 0.8417 (t80)
REVERT: C   57 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5821 (t80)
REVERT: C   65 TRP cc_start: 0.6428 (OUTLIER) cc_final: 0.4564 (t60)
REVERT: C  139 MET cc_start: 0.8243 (tpp) cc_final: 0.7871 (tpp)
REVERT: C  191 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8085 (tm-30)
REVERT: C  224 PHE cc_start: 0.6289 (t80) cc_final: 0.5685 (t80)
REVERT: A   57 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.5838 (t80)
REVERT: A   65 TRP cc_start: 0.6324 (OUTLIER) cc_final: 0.4453 (t60)
REVERT: A  139 MET cc_start: 0.8388 (tpp) cc_final: 0.7919 (tpp)
REVERT: A  191 GLU cc_start: 0.8617 (tm-30) cc_final: 0.7983 (tm-30)
REVERT: A  201 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8632 (mt)
REVERT: A  224 PHE cc_start: 0.6135 (t80) cc_final: 0.5592 (t80)
REVERT: B   57 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.5762 (t80)
REVERT: B   63 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8867 (mm)
REVERT: B   65 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.4491 (t60)
REVERT: B  138 VAL cc_start: 0.9489 (p) cc_final: 0.9190 (m)
REVERT: B  139 MET cc_start: 0.8305 (tpp) cc_final: 0.7769 (tpp)
REVERT: B  191 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: B  224 PHE cc_start: 0.6220 (t80) cc_final: 0.5648 (t80)
REVERT: B  230 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8841 (p)
REVERT: D   35 PHE cc_start: 0.8612 (t80) cc_final: 0.8198 (t80)
REVERT: D   57 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.5732 (t80)
REVERT: D   63 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8897 (mm)
REVERT: D   65 TRP cc_start: 0.6320 (OUTLIER) cc_final: 0.4489 (t60)
REVERT: D  139 MET cc_start: 0.8291 (tpp) cc_final: 0.7928 (tpp)
REVERT: D  191 GLU cc_start: 0.8642 (tm-30) cc_final: 0.7837 (tm-30)
REVERT: D  224 PHE cc_start: 0.6076 (t80) cc_final: 0.5554 (t80)
REVERT: D  230 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8782 (p)
  outliers start: 57
  outliers final: 33
  residues processed: 211
  average time/residue: 0.0676
  time to fit residues: 21.0411
Evaluate side-chains
  220 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 174
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   65 TRP
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 57 optimal weight:    0.1980
   chunk 64 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
C 225 ASN
A 225 ASN
B 101 HIS
B 225 ASN
D 225 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.150006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.113894 restraints weight = 12019.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.117054 restraints weight = 6988.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.119160 restraints weight = 4997.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120325 restraints weight = 4076.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121122 restraints weight = 3621.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7992  Z= 0.119
  Angle     :  0.562   8.384  10804  Z= 0.276
  Chirality :  0.040   0.141   1232
  Planarity :  0.003   0.029   1256
  Dihedral  : 17.560  95.043   1328
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  7.54 %
    Allowed  : 25.50 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.28), residues: 892
  helix: -0.37 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -2.84 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 122 
 TYR   0.016   0.001   TYR B  49 
 PHE   0.011   0.001   PHE D 224 
 TRP   0.008   0.001   TRP B  54 
 HIS   0.001   0.000   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7988)
  covalent geometry    : angle       0.56244 (10804)
  hydrogen bonds       : bond        0.03696 (  356)
  hydrogen bonds       : angle       4.45481 ( 1032)
  Misc. bond           : bond        0.00241 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 183
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8823 (t80) cc_final: 0.8524 (t80)
REVERT: C   57 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.5780 (t80)
REVERT: C   65 TRP cc_start: 0.6649 (OUTLIER) cc_final: 0.4736 (t60)
REVERT: C  138 VAL cc_start: 0.9480 (p) cc_final: 0.9224 (m)
REVERT: C  139 MET cc_start: 0.8229 (tpp) cc_final: 0.7813 (tpp)
REVERT: C  191 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8130 (tm-30)
REVERT: C  224 PHE cc_start: 0.6277 (t80) cc_final: 0.5684 (t80)
REVERT: A   57 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.5887 (t80)
REVERT: A   65 TRP cc_start: 0.6601 (OUTLIER) cc_final: 0.4706 (t60)
REVERT: A  138 VAL cc_start: 0.9475 (p) cc_final: 0.9222 (m)
REVERT: A  139 MET cc_start: 0.8387 (tpp) cc_final: 0.7814 (tpp)
REVERT: A  191 GLU cc_start: 0.8627 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: A  201 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8637 (mt)
REVERT: A  224 PHE cc_start: 0.6150 (t80) cc_final: 0.5579 (t80)
REVERT: A  230 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8841 (p)
REVERT: B   57 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5673 (t80)
REVERT: B   63 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8879 (mm)
REVERT: B   65 TRP cc_start: 0.6608 (OUTLIER) cc_final: 0.4748 (t60)
REVERT: B  139 MET cc_start: 0.8384 (tpp) cc_final: 0.7938 (tpp)
REVERT: B  191 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7862 (tm-30)
REVERT: B  224 PHE cc_start: 0.6290 (t80) cc_final: 0.5656 (t80)
REVERT: B  230 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8788 (p)
REVERT: D   35 PHE cc_start: 0.8718 (t80) cc_final: 0.8341 (t80)
REVERT: D   57 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.5776 (t80)
REVERT: D   65 TRP cc_start: 0.6641 (OUTLIER) cc_final: 0.4782 (t60)
REVERT: D  138 VAL cc_start: 0.9486 (p) cc_final: 0.9220 (m)
REVERT: D  139 MET cc_start: 0.8253 (tpp) cc_final: 0.7851 (tpp)
REVERT: D  191 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: D  224 PHE cc_start: 0.6065 (t80) cc_final: 0.5577 (t80)
REVERT: D  230 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8734 (p)
  outliers start: 60
  outliers final: 37
  residues processed: 206
  average time/residue: 0.0706
  time to fit residues: 21.1886
Evaluate side-chains
  229 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 179
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   65 TRP
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0170
   chunk 59 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0050
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.3832

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

Flipped N/Q/H residues before XYZ refinement:
B 225 ASN
D 225 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.153381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.118961 restraints weight = 11752.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.122244 restraints weight = 6633.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.124273 restraints weight = 4665.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.125707 restraints weight = 3772.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.126429 restraints weight = 3308.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7992  Z= 0.101
  Angle     :  0.546   7.603  10804  Z= 0.266
  Chirality :  0.040   0.151   1232
  Planarity :  0.003   0.030   1256
  Dihedral  : 16.938  89.772   1328
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  7.91 %
    Allowed  : 26.26 %
    Favored  : 65.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.28), residues: 892
  helix: -0.21 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.85 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 122 
 TYR   0.012   0.001   TYR B  49 
 PHE   0.010   0.001   PHE C  85 
 TRP   0.007   0.001   TRP B  54 
 HIS   0.001   0.000   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 7988)
  covalent geometry    : angle       0.54596 (10804)
  hydrogen bonds       : bond        0.03343 (  356)
  hydrogen bonds       : angle       4.36816 ( 1032)
  Misc. bond           : bond        0.00404 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 183
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4082 (OUTLIER) cc_final: 0.3524 (mt)
REVERT: C   35 PHE cc_start: 0.8743 (t80) cc_final: 0.8492 (t80)
REVERT: C   57 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.5743 (t80)
REVERT: C  115 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8146 (tt)
REVERT: C  139 MET cc_start: 0.8140 (tpp) cc_final: 0.7869 (tpp)
REVERT: C  191 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: C  224 PHE cc_start: 0.6194 (t80) cc_final: 0.5636 (t80)
REVERT: C  230 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8761 (p)
REVERT: A   19 ILE cc_start: 0.4243 (OUTLIER) cc_final: 0.3765 (mt)
REVERT: A   57 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5748 (t80)
REVERT: A  139 MET cc_start: 0.8377 (tpp) cc_final: 0.7947 (tpp)
REVERT: A  191 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7881 (tm-30)
REVERT: A  224 PHE cc_start: 0.5959 (t80) cc_final: 0.5474 (t80)
REVERT: A  230 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8733 (p)
REVERT: B   19 ILE cc_start: 0.4115 (OUTLIER) cc_final: 0.3584 (mt)
REVERT: B   57 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.5755 (t80)
REVERT: B   63 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8829 (mm)
REVERT: B  138 VAL cc_start: 0.9470 (p) cc_final: 0.9255 (m)
REVERT: B  139 MET cc_start: 0.8419 (tpp) cc_final: 0.7898 (tpp)
REVERT: B  187 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8769 (p)
REVERT: B  191 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7871 (tm-30)
REVERT: B  224 PHE cc_start: 0.6154 (t80) cc_final: 0.5554 (t80)
REVERT: B  230 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8659 (p)
REVERT: D   19 ILE cc_start: 0.4024 (OUTLIER) cc_final: 0.3251 (mm)
REVERT: D   35 PHE cc_start: 0.8650 (t80) cc_final: 0.8319 (t80)
REVERT: D   57 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.5735 (t80)
REVERT: D  139 MET cc_start: 0.8199 (tpp) cc_final: 0.7913 (tpp)
REVERT: D  190 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7659 (mm)
REVERT: D  191 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: D  224 PHE cc_start: 0.6049 (t80) cc_final: 0.5540 (t80)
REVERT: D  230 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8588 (p)
  outliers start: 63
  outliers final: 34
  residues processed: 212
  average time/residue: 0.0656
  time to fit residues: 20.7325
Evaluate side-chains
  216 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 166
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 51 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0470
   chunk 79 optimal weight:    0.0270
   chunk 72 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
D 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.153623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.117885 restraints weight = 11803.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.121231 restraints weight = 6740.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.123397 restraints weight = 4764.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.124630 restraints weight = 3864.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.125456 restraints weight = 3417.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7992  Z= 0.100
  Angle     :  0.538   7.771  10804  Z= 0.263
  Chirality :  0.040   0.192   1232
  Planarity :  0.003   0.036   1256
  Dihedral  : 16.062  89.377   1320
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  7.79 %
    Allowed  : 26.63 %
    Favored  : 65.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.28), residues: 892
  helix: -0.17 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -2.94 (0.33), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 122 
 TYR   0.010   0.001   TYR D  49 
 PHE   0.010   0.001   PHE A  85 
 TRP   0.007   0.001   TRP B  54 
 HIS   0.001   0.000   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7988)
  covalent geometry    : angle       0.53808 (10804)
  hydrogen bonds       : bond        0.03230 (  356)
  hydrogen bonds       : angle       4.34140 ( 1032)
  Misc. bond           : bond        0.00247 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 196
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4116 (OUTLIER) cc_final: 0.3398 (mm)
REVERT: C   35 PHE cc_start: 0.8738 (t80) cc_final: 0.8475 (t80)
REVERT: C   57 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.5834 (t80)
REVERT: C  115 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8096 (tt)
REVERT: C  139 MET cc_start: 0.8068 (tpp) cc_final: 0.7804 (tpp)
REVERT: C  191 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: C  224 PHE cc_start: 0.6138 (t80) cc_final: 0.5620 (t80)
REVERT: C  230 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8733 (p)
REVERT: A   19 ILE cc_start: 0.4203 (OUTLIER) cc_final: 0.3514 (mm)
REVERT: A   57 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.5896 (t80)
REVERT: A  139 MET cc_start: 0.8363 (tpp) cc_final: 0.7939 (tpp)
REVERT: A  191 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7878 (tm-30)
REVERT: A  224 PHE cc_start: 0.5929 (t80) cc_final: 0.5380 (t80)
REVERT: A  230 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8692 (p)
REVERT: B   19 ILE cc_start: 0.4073 (OUTLIER) cc_final: 0.3326 (mm)
REVERT: B   57 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.5967 (t80)
REVERT: B  139 MET cc_start: 0.8389 (tpp) cc_final: 0.7950 (tpp)
REVERT: B  187 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8855 (p)
REVERT: B  191 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: B  224 PHE cc_start: 0.6100 (t80) cc_final: 0.5478 (t80)
REVERT: B  230 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8632 (p)
REVERT: D   19 ILE cc_start: 0.3974 (OUTLIER) cc_final: 0.3223 (mm)
REVERT: D   35 PHE cc_start: 0.8638 (t80) cc_final: 0.8330 (t80)
REVERT: D   57 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.5827 (t80)
REVERT: D  139 MET cc_start: 0.8215 (tpp) cc_final: 0.7924 (tpp)
REVERT: D  191 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: D  224 PHE cc_start: 0.6122 (t80) cc_final: 0.5615 (t80)
REVERT: D  230 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8546 (p)
  outliers start: 62
  outliers final: 37
  residues processed: 221
  average time/residue: 0.0667
  time to fit residues: 21.8797
Evaluate side-chains
  227 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 176
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.151017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114286 restraints weight = 11946.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.117594 restraints weight = 6919.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.119568 restraints weight = 4940.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120843 restraints weight = 4043.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.121735 restraints weight = 3594.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7992  Z= 0.130
  Angle     :  0.573   7.681  10804  Z= 0.280
  Chirality :  0.042   0.195   1232
  Planarity :  0.003   0.037   1256
  Dihedral  : 15.908  89.824   1320
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  7.79 %
    Allowed  : 28.39 %
    Favored  : 63.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.28), residues: 892
  helix: -0.23 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -2.78 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 122 
 TYR   0.009   0.001   TYR D  49 
 PHE   0.022   0.001   PHE A  35 
 TRP   0.025   0.001   TRP D 193 
 HIS   0.001   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7988)
  covalent geometry    : angle       0.57344 (10804)
  hydrogen bonds       : bond        0.03462 (  356)
  hydrogen bonds       : angle       4.37793 ( 1032)
  Misc. bond           : bond        0.00236 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 180
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4164 (OUTLIER) cc_final: 0.3436 (mm)
REVERT: C   35 PHE cc_start: 0.8780 (t80) cc_final: 0.8491 (t80)
REVERT: C   57 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5808 (t80)
REVERT: C  139 MET cc_start: 0.8119 (tpp) cc_final: 0.7850 (tpp)
REVERT: C  224 PHE cc_start: 0.6214 (t80) cc_final: 0.5673 (t80)
REVERT: A   19 ILE cc_start: 0.4233 (OUTLIER) cc_final: 0.3519 (mm)
REVERT: A   57 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.5863 (t80)
REVERT: A  139 MET cc_start: 0.8295 (tpp) cc_final: 0.7945 (tpp)
REVERT: A  191 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: A  224 PHE cc_start: 0.6025 (t80) cc_final: 0.5445 (t80)
REVERT: A  230 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8750 (p)
REVERT: B   19 ILE cc_start: 0.4135 (OUTLIER) cc_final: 0.3382 (mm)
REVERT: B   57 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.5787 (t80)
REVERT: B  139 MET cc_start: 0.8439 (tpp) cc_final: 0.7992 (tpp)
REVERT: B  191 GLU cc_start: 0.8643 (tm-30) cc_final: 0.7919 (tm-30)
REVERT: B  224 PHE cc_start: 0.6199 (t80) cc_final: 0.5571 (t80)
REVERT: B  230 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8700 (p)
REVERT: D   19 ILE cc_start: 0.4037 (OUTLIER) cc_final: 0.3262 (mm)
REVERT: D   35 PHE cc_start: 0.8679 (t80) cc_final: 0.8306 (t80)
REVERT: D   57 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.5785 (t80)
REVERT: D  139 MET cc_start: 0.8255 (tpp) cc_final: 0.7986 (tpp)
REVERT: D  191 GLU cc_start: 0.8601 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: D  224 PHE cc_start: 0.6045 (t80) cc_final: 0.5580 (t80)
REVERT: D  230 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8637 (p)
  outliers start: 62
  outliers final: 38
  residues processed: 211
  average time/residue: 0.0639
  time to fit residues: 20.3170
Evaluate side-chains
  224 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 175
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 75 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.150257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113158 restraints weight = 11849.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.116360 restraints weight = 7014.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.118479 restraints weight = 5062.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.119659 restraints weight = 4132.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.120444 restraints weight = 3672.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7992  Z= 0.144
  Angle     :  0.601   7.921  10804  Z= 0.296
  Chirality :  0.043   0.185   1232
  Planarity :  0.004   0.039   1256
  Dihedral  : 15.955  89.887   1320
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 30.03 %
    Favored  : 63.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.28), residues: 892
  helix: -0.42 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.71 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 122 
 TYR   0.008   0.001   TYR A  49 
 PHE   0.024   0.001   PHE B  35 
 TRP   0.019   0.001   TRP D 193 
 HIS   0.001   0.001   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7988)
  covalent geometry    : angle       0.60121 (10804)
  hydrogen bonds       : bond        0.03568 (  356)
  hydrogen bonds       : angle       4.39702 ( 1032)
  Misc. bond           : bond        0.00208 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 185
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4151 (OUTLIER) cc_final: 0.3437 (mm)
REVERT: C   35 PHE cc_start: 0.8755 (t80) cc_final: 0.8471 (t80)
REVERT: C   57 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.5831 (t80)
REVERT: C  139 MET cc_start: 0.8146 (tpp) cc_final: 0.7913 (tpp)
REVERT: C  224 PHE cc_start: 0.6253 (t80) cc_final: 0.5708 (t80)
REVERT: A   19 ILE cc_start: 0.4313 (OUTLIER) cc_final: 0.3616 (mm)
REVERT: A   57 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.5852 (t80)
REVERT: A  139 MET cc_start: 0.8281 (tpp) cc_final: 0.7939 (tpp)
REVERT: A  191 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: A  224 PHE cc_start: 0.6061 (t80) cc_final: 0.5489 (t80)
REVERT: B   19 ILE cc_start: 0.4125 (OUTLIER) cc_final: 0.3373 (mm)
REVERT: B   57 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.5827 (t80)
REVERT: B  139 MET cc_start: 0.8402 (tpp) cc_final: 0.8178 (tpp)
REVERT: B  191 GLU cc_start: 0.8642 (tm-30) cc_final: 0.7971 (tm-30)
REVERT: B  224 PHE cc_start: 0.6242 (t80) cc_final: 0.5611 (t80)
REVERT: D   19 ILE cc_start: 0.4019 (OUTLIER) cc_final: 0.3255 (mm)
REVERT: D   35 PHE cc_start: 0.8598 (t80) cc_final: 0.8261 (t80)
REVERT: D   57 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.5789 (t80)
REVERT: D  191 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8012 (tm-30)
REVERT: D  224 PHE cc_start: 0.6065 (t80) cc_final: 0.5604 (t80)
  outliers start: 54
  outliers final: 38
  residues processed: 211
  average time/residue: 0.0620
  time to fit residues: 19.4885
Evaluate side-chains
  224 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 178
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    0.0170
   chunk 74 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 45 optimal weight:    0.1980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.4018

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.153553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.117514 restraints weight = 11631.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.120674 restraints weight = 6813.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.122847 restraints weight = 4844.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.124061 restraints weight = 3938.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.124673 restraints weight = 3478.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7992  Z= 0.108
  Angle     :  0.582   8.023  10804  Z= 0.286
  Chirality :  0.042   0.186   1232
  Planarity :  0.004   0.039   1256
  Dihedral  : 15.571  89.950   1320
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 31.28 %
    Favored  : 62.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.28), residues: 892
  helix: -0.40 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.80 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 122 
 TYR   0.008   0.001   TYR B  49 
 PHE   0.024   0.001   PHE D 215 
 TRP   0.022   0.001   TRP D 193 
 HIS   0.001   0.000   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7988)
  covalent geometry    : angle       0.58151 (10804)
  hydrogen bonds       : bond        0.03345 (  356)
  hydrogen bonds       : angle       4.37739 ( 1032)
  Misc. bond           : bond        0.00144 (    4)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 189
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4077 (OUTLIER) cc_final: 0.3383 (mm)
REVERT: C   35 PHE cc_start: 0.8693 (t80) cc_final: 0.8493 (t80)
REVERT: C   57 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.5731 (t80)
REVERT: C  139 MET cc_start: 0.8120 (tpp) cc_final: 0.7900 (tpp)
REVERT: C  217 LEU cc_start: 0.8906 (mt) cc_final: 0.8706 (mt)
REVERT: C  224 PHE cc_start: 0.6200 (t80) cc_final: 0.5669 (t80)
REVERT: C  230 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8699 (p)
REVERT: A   19 ILE cc_start: 0.4289 (OUTLIER) cc_final: 0.3588 (mm)
REVERT: A   57 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.5778 (t80)
REVERT: A  139 MET cc_start: 0.8329 (tpp) cc_final: 0.7996 (tpp)
REVERT: A  191 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: A  217 LEU cc_start: 0.8944 (mt) cc_final: 0.8734 (mt)
REVERT: A  224 PHE cc_start: 0.5965 (t80) cc_final: 0.5412 (t80)
REVERT: A  230 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8642 (p)
REVERT: B   19 ILE cc_start: 0.4058 (OUTLIER) cc_final: 0.3332 (mm)
REVERT: B   57 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5709 (t80)
REVERT: B  139 MET cc_start: 0.8378 (tpp) cc_final: 0.7800 (tpp)
REVERT: B  191 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7998 (tm-30)
REVERT: B  224 PHE cc_start: 0.6158 (t80) cc_final: 0.5544 (t80)
REVERT: B  230 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8607 (p)
REVERT: D   19 ILE cc_start: 0.3956 (OUTLIER) cc_final: 0.3198 (mm)
REVERT: D   35 PHE cc_start: 0.8625 (t80) cc_final: 0.8330 (t80)
REVERT: D   57 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.5744 (t80)
REVERT: D  139 MET cc_start: 0.8088 (tpp) cc_final: 0.7563 (mtt)
REVERT: D  191 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: D  224 PHE cc_start: 0.6091 (t80) cc_final: 0.5559 (t80)
REVERT: D  230 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8556 (p)
  outliers start: 48
  outliers final: 28
  residues processed: 207
  average time/residue: 0.0647
  time to fit residues: 20.0891
Evaluate side-chains
  214 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 174
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  164 MET
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.0270
   chunk 39 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0030
   chunk 42 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0060
   overall best weight:    0.2464

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.156104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.120261 restraints weight = 11710.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.123497 restraints weight = 6793.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.125546 restraints weight = 4835.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.126922 restraints weight = 3925.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.127917 restraints weight = 3435.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7992  Z= 0.106
  Angle     :  0.609   9.379  10804  Z= 0.291
  Chirality :  0.042   0.182   1232
  Planarity :  0.004   0.039   1256
  Dihedral  : 15.238  89.696   1320
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 32.41 %
    Favored  : 62.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.27), residues: 892
  helix: -0.33 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.82 (0.33), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 122 
 TYR   0.008   0.001   TYR D  49 
 PHE   0.034   0.001   PHE B  35 
 TRP   0.023   0.001   TRP B 193 
 HIS   0.001   0.000   HIS D  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7988)
  covalent geometry    : angle       0.60893 (10804)
  hydrogen bonds       : bond        0.03151 (  356)
  hydrogen bonds       : angle       4.30259 ( 1032)
  Misc. bond           : bond        0.00115 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1471.69 seconds
wall clock time: 25 minutes 54.60 seconds (1554.60 seconds total)