Starting phenix.real_space_refine
on Fri Mar 14 05:47:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vsc_21376/03_2025/6vsc_21376.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vsc_21376/03_2025/6vsc_21376.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2025/6vsc_21376.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2025/6vsc_21376.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2025/6vsc_21376.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vsc_21376/03_2025/6vsc_21376.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 sd=   0.111
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    6230      2.51       5
     N    1610      2.21       5
     O    1780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9670
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "V"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1934
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
    Chain: "W"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1934
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
    Chain: "X"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1934
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1934
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
    Chain: "Z"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1934
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
  Time building chain proxies: 5.97, per 1000 atoms: 0.62
  Number of scatterers: 9670
  At special positions: 0
  Unit cell: (101.01, 98.28, 76.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1780      8.00
     N    1610      7.00
     C    6230      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.68
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 10 sheets defined
      46.0% alpha, 30.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'V' and resid 21 through 28
    Processing helix  chain 'V' and resid 29 through 53
    Processing helix  chain 'V' and resid 78 through 91
    Processing helix  chain 'V' and resid 92 through 96
    Processing helix  chain 'V' and resid 124 through 132
    Processing helix  chain 'V' and resid 160 through 178
      removed outlier: 3.615A  pdb=" N   ALA V 170 " --> pdb=" O   GLU V 166 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   HIS V 171 " --> pdb=" O   LEU V 167 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TYR V 178 " --> pdb=" O   THR V 174 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 206 through 217
      removed outlier: 3.786A  pdb=" N   LYS V 210 " --> pdb=" O   ALA V 206 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 219 through 225
    Processing helix  chain 'V' and resid 238 through 240
      No H-bonds generated for 'chain 'V' and resid 238 through 240'
    Processing helix  chain 'V' and resid 241 through 246
    Processing helix  chain 'W' and resid 21 through 28
    Processing helix  chain 'W' and resid 29 through 53
    Processing helix  chain 'W' and resid 78 through 91
    Processing helix  chain 'W' and resid 92 through 96
    Processing helix  chain 'W' and resid 124 through 132
    Processing helix  chain 'W' and resid 160 through 178
      removed outlier: 3.616A  pdb=" N   ALA W 170 " --> pdb=" O   GLU W 166 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS W 171 " --> pdb=" O   LEU W 167 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR W 178 " --> pdb=" O   THR W 174 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 206 through 217
      removed outlier: 3.784A  pdb=" N   LYS W 210 " --> pdb=" O   ALA W 206 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 219 through 225
    Processing helix  chain 'W' and resid 238 through 240
      No H-bonds generated for 'chain 'W' and resid 238 through 240'
    Processing helix  chain 'W' and resid 241 through 246
    Processing helix  chain 'X' and resid 21 through 28
    Processing helix  chain 'X' and resid 29 through 53
    Processing helix  chain 'X' and resid 78 through 91
    Processing helix  chain 'X' and resid 92 through 96
    Processing helix  chain 'X' and resid 124 through 132
    Processing helix  chain 'X' and resid 160 through 178
      removed outlier: 3.615A  pdb=" N   ALA X 170 " --> pdb=" O   GLU X 166 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   HIS X 171 " --> pdb=" O   LEU X 167 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TYR X 178 " --> pdb=" O   THR X 174 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 206 through 217
      removed outlier: 3.782A  pdb=" N   LYS X 210 " --> pdb=" O   ALA X 206 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 219 through 225
    Processing helix  chain 'X' and resid 238 through 240
      No H-bonds generated for 'chain 'X' and resid 238 through 240'
    Processing helix  chain 'X' and resid 241 through 246
    Processing helix  chain 'Y' and resid 21 through 28
    Processing helix  chain 'Y' and resid 29 through 53
    Processing helix  chain 'Y' and resid 78 through 91
    Processing helix  chain 'Y' and resid 92 through 96
    Processing helix  chain 'Y' and resid 124 through 132
      removed outlier: 6.025A  pdb=" N   ARG Y 130 " --> pdb=" O   GLU Y 126 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 160 through 178
      removed outlier: 3.612A  pdb=" N   ALA Y 170 " --> pdb=" O   GLU Y 166 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS Y 171 " --> pdb=" O   LEU Y 167 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR Y 178 " --> pdb=" O   THR Y 174 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 206 through 217
      removed outlier: 3.779A  pdb=" N   LYS Y 210 " --> pdb=" O   ALA Y 206 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 219 through 225
    Processing helix  chain 'Y' and resid 238 through 240
      No H-bonds generated for 'chain 'Y' and resid 238 through 240'
    Processing helix  chain 'Y' and resid 241 through 246
    Processing helix  chain 'Z' and resid 21 through 28
    Processing helix  chain 'Z' and resid 29 through 53
    Processing helix  chain 'Z' and resid 78 through 91
    Processing helix  chain 'Z' and resid 92 through 96
    Processing helix  chain 'Z' and resid 124 through 132
    Processing helix  chain 'Z' and resid 160 through 178
      removed outlier: 3.617A  pdb=" N   ALA Z 170 " --> pdb=" O   GLU Z 166 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   HIS Z 171 " --> pdb=" O   LEU Z 167 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR Z 178 " --> pdb=" O   THR Z 174 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 206 through 217
      removed outlier: 3.785A  pdb=" N   LYS Z 210 " --> pdb=" O   ALA Z 206 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 219 through 225
    Processing helix  chain 'Z' and resid 238 through 240
      No H-bonds generated for 'chain 'Z' and resid 238 through 240'
    Processing helix  chain 'Z' and resid 241 through 246
    Processing sheet with id=AA1, first strand: chain 'V' and resid 226 through 228
      removed outlier: 4.168A  pdb=" N   TRP V  11 " --> pdb=" O   VAL V 108 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   THR V  19 " --> pdb=" O   PRO V 100 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU V 109 " --> pdb=" O   ILE V 186 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   ILE V 186 " --> pdb=" O   GLU V 109 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'V' and resid 150 through 151
    Processing sheet with id=AA3, first strand: chain 'W' and resid 226 through 228
      removed outlier: 5.941A  pdb=" N   ASP W   9 " --> pdb=" O   LEU W 110 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   LEU W 110 " --> pdb=" O   ASP W   9 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   TRP W  11 " --> pdb=" O   VAL W 108 " (cutoff:3.500A)
      removed outlier: 4.812A  pdb=" N   THR W  19 " --> pdb=" O   PRO W 100 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLU W 109 " --> pdb=" O   ILE W 186 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   ILE W 186 " --> pdb=" O   GLU W 109 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'W' and resid 150 through 151
    Processing sheet with id=AA5, first strand: chain 'X' and resid 226 through 228
      removed outlier: 5.937A  pdb=" N   ASP X   9 " --> pdb=" O   LEU X 110 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU X 110 " --> pdb=" O   ASP X   9 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   TRP X  11 " --> pdb=" O   VAL X 108 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   THR X  19 " --> pdb=" O   PRO X 100 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU X 109 " --> pdb=" O   ILE X 186 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   ILE X 186 " --> pdb=" O   GLU X 109 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'X' and resid 150 through 151
    Processing sheet with id=AA7, first strand: chain 'Y' and resid 226 through 228
      removed outlier: 5.941A  pdb=" N   ASP Y   9 " --> pdb=" O   LEU Y 110 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   LEU Y 110 " --> pdb=" O   ASP Y   9 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   TRP Y  11 " --> pdb=" O   VAL Y 108 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   THR Y  19 " --> pdb=" O   PRO Y 100 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLU Y 109 " --> pdb=" O   ILE Y 186 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   ILE Y 186 " --> pdb=" O   GLU Y 109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'Y' and resid 150 through 151
    Processing sheet with id=AA9, first strand: chain 'Z' and resid 226 through 228
      removed outlier: 5.937A  pdb=" N   ASP Z   9 " --> pdb=" O   LEU Z 110 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LEU Z 110 " --> pdb=" O   ASP Z   9 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   TRP Z  11 " --> pdb=" O   VAL Z 108 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   THR Z  19 " --> pdb=" O   PRO Z 100 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLU Z 109 " --> pdb=" O   ILE Z 186 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   ILE Z 186 " --> pdb=" O   GLU Z 109 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'Z' and resid 150 through 151

    564 hydrogen bonds defined for protein.
    1557 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.18 -     1.33: 2284
        1.33 -     1.47: 3464
        1.47 -     1.62: 4082
        1.62 -     1.76: 5
        1.76 -     1.90: 85
  Bond restraints: 9920
  Sorted by residual:
  bond pdb=" CE1 HIS Z  83 "
       pdb=" NE2 HIS Z  83 "
    ideal  model  delta    sigma   weight residual
    1.321  1.389 -0.068 1.00e-02 1.00e+04 4.66e+01
  bond pdb=" CE1 HIS X  83 "
       pdb=" NE2 HIS X  83 "
    ideal  model  delta    sigma   weight residual
    1.321  1.387 -0.066 1.00e-02 1.00e+04 4.35e+01
  bond pdb=" CE1 HIS Y  83 "
       pdb=" NE2 HIS Y  83 "
    ideal  model  delta    sigma   weight residual
    1.321  1.387 -0.066 1.00e-02 1.00e+04 4.29e+01
  bond pdb=" CE1 HIS V  83 "
       pdb=" NE2 HIS V  83 "
    ideal  model  delta    sigma   weight residual
    1.321  1.385 -0.064 1.00e-02 1.00e+04 4.04e+01
  bond pdb=" CE1 HIS W  83 "
       pdb=" NE2 HIS W  83 "
    ideal  model  delta    sigma   weight residual
    1.321  1.382 -0.061 1.00e-02 1.00e+04 3.66e+01
  ... (remaining 9915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 11665
        3.41 -     6.81: 1516
        6.81 -    10.22: 203
       10.22 -    13.63: 34
       13.63 -    17.03: 7
  Bond angle restraints: 13425
  Sorted by residual:
  angle pdb=" CA  PRO V 121 "
        pdb=" N   PRO V 121 "
        pdb=" CD  PRO V 121 "
      ideal   model   delta    sigma   weight residual
     112.00   99.20   12.80 1.40e+00 5.10e-01 8.36e+01
  angle pdb=" CG  ARG Y 164 "
        pdb=" CD  ARG Y 164 "
        pdb=" NE  ARG Y 164 "
      ideal   model   delta    sigma   weight residual
     112.00   94.97   17.03 2.20e+00 2.07e-01 5.99e+01
  angle pdb=" CG  ARG W 164 "
        pdb=" CD  ARG W 164 "
        pdb=" NE  ARG W 164 "
      ideal   model   delta    sigma   weight residual
     112.00   95.09   16.91 2.20e+00 2.07e-01 5.91e+01
  angle pdb=" CG  ARG V 164 "
        pdb=" CD  ARG V 164 "
        pdb=" NE  ARG V 164 "
      ideal   model   delta    sigma   weight residual
     112.00   95.18   16.82 2.20e+00 2.07e-01 5.85e+01
  angle pdb=" CG  ARG X 164 "
        pdb=" CD  ARG X 164 "
        pdb=" NE  ARG X 164 "
      ideal   model   delta    sigma   weight residual
     112.00   95.22   16.78 2.20e+00 2.07e-01 5.82e+01
  ... (remaining 13420 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4897
       17.82 -    35.64: 713
       35.64 -    53.45: 174
       53.45 -    71.27: 52
       71.27 -    89.09: 14
  Dihedral angle restraints: 5850
    sinusoidal: 2405
      harmonic: 3445
  Sorted by residual:
  dihedral pdb=" C   MET Z 146 "
           pdb=" N   MET Z 146 "
           pdb=" CA  MET Z 146 "
           pdb=" CB  MET Z 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.00  -20.60     0      2.50e+00 1.60e-01 6.79e+01
  dihedral pdb=" C   VAL Z 221 "
           pdb=" N   VAL Z 221 "
           pdb=" CA  VAL Z 221 "
           pdb=" CB  VAL Z 221 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -142.46   20.46     0      2.50e+00 1.60e-01 6.69e+01
  dihedral pdb=" N   VAL Z 221 "
           pdb=" C   VAL Z 221 "
           pdb=" CA  VAL Z 221 "
           pdb=" CB  VAL Z 221 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  143.85  -20.45     0      2.50e+00 1.60e-01 6.69e+01
  ... (remaining 5847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.161: 1099
       0.161 -    0.321: 272
       0.321 -    0.482: 52
       0.482 -    0.642: 1
       0.642 -    0.803: 6
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" CA  VAL Z 221 "
            pdb=" N   VAL Z 221 "
            pdb=" C   VAL Z 221 "
            pdb=" CB  VAL Z 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.64    0.80 2.00e-01 2.50e+01 1.61e+01
  chirality pdb=" CA  VAL X 221 "
            pdb=" N   VAL X 221 "
            pdb=" C   VAL X 221 "
            pdb=" CB  VAL X 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.64    0.80 2.00e-01 2.50e+01 1.60e+01
  chirality pdb=" CA  VAL V 221 "
            pdb=" N   VAL V 221 "
            pdb=" C   VAL V 221 "
            pdb=" CB  VAL V 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.64    0.80 2.00e-01 2.50e+01 1.60e+01
  ... (remaining 1427 not shown)

  Planarity restraints: 1705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR Y 178 "    0.030 2.00e-02 2.50e+03   6.15e-02 3.78e+01
        pdb=" C   TYR Y 178 "   -0.106 2.00e-02 2.50e+03
        pdb=" O   TYR Y 178 "    0.040 2.00e-02 2.50e+03
        pdb=" N   ALA Y 179 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE Z 225 "   -0.035 2.00e-02 2.50e+03   4.59e-02 3.69e+01
        pdb=" CG  PHE Z 225 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 PHE Z 225 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE Z 225 "    0.046 2.00e-02 2.50e+03
        pdb=" CE1 PHE Z 225 "    0.058 2.00e-02 2.50e+03
        pdb=" CE2 PHE Z 225 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  PHE Z 225 "   -0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE W 225 "    0.035 2.00e-02 2.50e+03   4.58e-02 3.67e+01
        pdb=" CG  PHE W 225 "    0.005 2.00e-02 2.50e+03
        pdb=" CD1 PHE W 225 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE W 225 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE1 PHE W 225 "   -0.057 2.00e-02 2.50e+03
        pdb=" CE2 PHE W 225 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE W 225 "    0.088 2.00e-02 2.50e+03
  ... (remaining 1702 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 986
        2.70 -     3.25: 9413
        3.25 -     3.80: 18076
        3.80 -     4.35: 24730
        4.35 -     4.90: 38445
  Nonbonded interactions: 91650
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS V  67 "
            pdb=" OD1 ASP W 194 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" NZ  LYS W  67 "
            pdb=" OD1 ASP Y 194 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" NZ  LYS X  67 "
            pdb=" OD1 ASP Z 194 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OD1 ASP X 194 "
            pdb=" NZ  LYS Y  67 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" OD1 ASP V 194 "
            pdb=" NZ  LYS Z  67 "
     model   vdw
     2.186 3.120
  ... (remaining 91645 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
  selection = chain 'Y'
  selection = chain 'Z'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.920
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  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:12.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8905
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      :  0.014   0.126   9920  Z= 0.903
  Angle     :  2.410  17.031  13425  Z= 1.576
  Chirality :  0.153   0.803   1430
  Planarity :  0.012   0.061   1705
  Dihedral  : 18.437  89.087   3630
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  7.73 %
    Allowed  : 11.59 %
    Favored  : 80.68 %
  Cbeta Deviations :  6.76 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.23), residues: 1155
  helix: -2.12 (0.18), residues: 510
  sheet:  0.21 (0.29), residues: 320
  loop : -1.01 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.012   TRP W  25 
 HIS   0.018   0.007   HIS W  58 
 PHE   0.088   0.016   PHE Z 225 
 TYR   0.053   0.011   TYR X 140 
 ARG   0.030   0.005   ARG Y 129 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  433 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 353
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   34 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8897 (tm-30)
REVERT: V  109 GLU cc_start: 0.8648 (pt0) cc_final: 0.8330 (pm20)
REVERT: V  110 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6810 (mp)
REVERT: V  130 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8244 (ttp-170)
REVERT: V  147 ASP cc_start: 0.9198 (m-30) cc_final: 0.8951 (m-30)
REVERT: V  153 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7276 (p0)
REVERT: V  181 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8024 (mmtm)
REVERT: V  184 GLN cc_start: 0.9078 (tt0) cc_final: 0.8779 (pm20)
REVERT: V  196 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8965 (mt-10)
REVERT: V  210 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9028 (tmmt)
REVERT: W   30 ASN cc_start: 0.8802 (t0) cc_final: 0.8386 (t0)
REVERT: W  105 VAL cc_start: 0.9154 (t) cc_final: 0.8913 (p)
REVERT: W  123 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7885 (mp-120)
REVERT: W  165 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8036 (mtm110)
REVERT: W  181 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8027 (mmtp)
REVERT: W  205 ASP cc_start: 0.9150 (t0) cc_final: 0.8917 (t0)
REVERT: X   33 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8703 (mtm110)
REVERT: X   34 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8758 (tm-30)
REVERT: X  130 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8435 (ttp-170)
REVERT: X  181 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (mtpm)
REVERT: X  184 GLN cc_start: 0.9169 (tt0) cc_final: 0.8840 (pm20)
REVERT: Y  128 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8402 (mmp-170)
REVERT: Y  129 ARG cc_start: 0.8961 (ttp-110) cc_final: 0.8489 (ttm-80)
REVERT: Y  130 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8365 (ttt180)
REVERT: Y  147 ASP cc_start: 0.9174 (m-30) cc_final: 0.8588 (m-30)
REVERT: Y  151 GLN cc_start: 0.9099 (mm110) cc_final: 0.8898 (tt0)
REVERT: Y  165 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8155 (mtm110)
REVERT: Y  181 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8449 (mmmt)
REVERT: Y  184 GLN cc_start: 0.9202 (tt0) cc_final: 0.8904 (pm20)
REVERT: Z   30 ASN cc_start: 0.8947 (t0) cc_final: 0.8514 (t0)
REVERT: Z  109 GLU cc_start: 0.8653 (pt0) cc_final: 0.8355 (pm20)
REVERT: Z  110 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7038 (mp)
REVERT: Z  128 ARG cc_start: 0.8743 (tpt170) cc_final: 0.8513 (mmm160)
REVERT: Z  151 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8879 (tt0)
REVERT: Z  165 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7656 (mtm110)
REVERT: Z  181 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (mtpm)
REVERT: Z  184 GLN cc_start: 0.9159 (tt0) cc_final: 0.8937 (pm20)
REVERT: Z  210 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9079 (tmmt)
  outliers start: 80
  outliers final: 12
  residues processed: 405
  average time/residue: 1.4330
  time to fit residues: 615.8246
Evaluate side-chains
  284 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 260
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   67 LYS
Chi-restraints excluded: chain V residue  110 LEU
Chi-restraints excluded: chain V residue  153 ASN
Chi-restraints excluded: chain V residue  181 LYS
Chi-restraints excluded: chain V residue  210 LYS
Chi-restraints excluded: chain W residue    7 THR
Chi-restraints excluded: chain W residue   67 LYS
Chi-restraints excluded: chain W residue  123 GLN
Chi-restraints excluded: chain W residue  181 LYS
Chi-restraints excluded: chain W residue  233 VAL
Chi-restraints excluded: chain X residue   33 ARG
Chi-restraints excluded: chain X residue   67 LYS
Chi-restraints excluded: chain X residue  181 LYS
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   67 LYS
Chi-restraints excluded: chain Y residue  126 GLU
Chi-restraints excluded: chain Y residue  181 LYS
Chi-restraints excluded: chain Z residue    7 THR
Chi-restraints excluded: chain Z residue   71 LEU
Chi-restraints excluded: chain Z residue  110 LEU
Chi-restraints excluded: chain Z residue  153 ASN
Chi-restraints excluded: chain Z residue  181 LYS
Chi-restraints excluded: chain Z residue  210 LYS
Chi-restraints excluded: chain Z residue  233 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
V  30 ASN
V 247 HIS
W   6 GLN
W 247 HIS
X  55 GLN
X 247 HIS
Y 247 HIS
Z  55 GLN
Z 247 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.106902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.093797 restraints weight = 19223.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.20
r_work: 0.3321 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9920  Z= 0.252
  Angle     :  0.659   8.201  13425  Z= 0.346
  Chirality :  0.044   0.180   1430
  Planarity :  0.005   0.040   1705
  Dihedral  :  7.797  59.069   1369
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 21.26 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.23), residues: 1155
  helix: -0.02 (0.21), residues: 535
  sheet: -0.44 (0.26), residues: 365
  loop : -0.80 (0.35), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP Z 156 
 HIS   0.004   0.001   HIS Z 247 
 PHE   0.020   0.002   PHE Z 225 
 TYR   0.020   0.002   TYR Y 157 
 ARG   0.006   0.001   ARG V 149 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 341
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V  147 ASP cc_start: 0.8227 (m-30) cc_final: 0.8022 (m-30)
REVERT: V  153 ASN cc_start: 0.6873 (OUTLIER) cc_final: 0.6658 (p0)
REVERT: V  169 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7285 (ttp-170)
REVERT: V  216 MET cc_start: 0.8065 (mtm) cc_final: 0.7716 (mtp)
REVERT: W   30 ASN cc_start: 0.8232 (t0) cc_final: 0.7928 (t0)
REVERT: W  102 TYR cc_start: 0.8261 (t80) cc_final: 0.7970 (t80)
REVERT: W  129 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8161 (ttp-110)
REVERT: W  165 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7423 (mtm110)
REVERT: X   85 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9101 (mp)
REVERT: X  151 GLN cc_start: 0.8907 (tp40) cc_final: 0.8681 (tt0)
REVERT: X  196 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8015 (mt-10)
REVERT: X  210 LYS cc_start: 0.9220 (tmmt) cc_final: 0.8982 (tttm)
REVERT: X  216 MET cc_start: 0.8022 (mtm) cc_final: 0.7741 (mtp)
REVERT: Y  147 ASP cc_start: 0.8248 (m-30) cc_final: 0.7754 (m-30)
REVERT: Y  196 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7271 (mt-10)
REVERT: Y  216 MET cc_start: 0.8265 (mtm) cc_final: 0.7752 (mtp)
REVERT: Z  147 ASP cc_start: 0.8010 (m-30) cc_final: 0.7737 (m-30)
REVERT: Z  165 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.7046 (mtm110)
REVERT: Z  196 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7666 (mt-10)
REVERT: Z  216 MET cc_start: 0.8426 (mtm) cc_final: 0.7934 (mtm)
  outliers start: 56
  outliers final: 11
  residues processed: 376
  average time/residue: 1.1560
  time to fit residues: 465.0700
Evaluate side-chains
  307 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 293
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   37 ILE
Chi-restraints excluded: chain V residue  153 ASN
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  212 LEU
Chi-restraints excluded: chain W residue   37 ILE
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain X residue   85 ILE
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   67 LYS
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  239 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
V  30 ASN
V 153 ASN
V 247 HIS
X 247 HIS
Z  30 ASN
Z 241 ASN
Z 247 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.105164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.092180 restraints weight = 20468.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.32
r_work: 0.3333 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9920  Z= 0.387
  Angle     :  0.674   7.323  13425  Z= 0.345
  Chirality :  0.045   0.338   1430
  Planarity :  0.005   0.059   1705
  Dihedral  :  5.284  59.348   1307
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 22.80 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.24), residues: 1155
  helix:  0.43 (0.22), residues: 540
  sheet: -0.32 (0.26), residues: 330
  loop : -0.56 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP Z 156 
 HIS   0.004   0.001   HIS X  83 
 PHE   0.018   0.002   PHE X 143 
 TYR   0.024   0.002   TYR Y 157 
 ARG   0.008   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 296
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   55 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8153 (mp10)
REVERT: V  196 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8127 (mt-10)
REVERT: W   30 ASN cc_start: 0.8289 (t0) cc_final: 0.8023 (t0)
REVERT: W  105 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8663 (p)
REVERT: W  129 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.8136 (ttp-110)
REVERT: W  165 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7494 (mtm110)
REVERT: W  207 LEU cc_start: 0.8831 (tp) cc_final: 0.8561 (tm)
REVERT: X   85 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9099 (mp)
REVERT: X  146 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8862 (ptt)
REVERT: X  196 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8055 (mt-10)
REVERT: Y  174 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7124 (p)
REVERT: Z   30 ASN cc_start: 0.8251 (t0) cc_final: 0.7977 (t0)
REVERT: Z  161 MET cc_start: 0.7321 (mpt) cc_final: 0.7027 (mpt)
REVERT: Z  165 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.7118 (mtm110)
REVERT: Z  193 ASP cc_start: 0.8648 (t70) cc_final: 0.8425 (t0)
  outliers start: 55
  outliers final: 27
  residues processed: 326
  average time/residue: 1.1723
  time to fit residues: 409.5054
Evaluate side-chains
  302 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 271
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   14 LEU
Chi-restraints excluded: chain V residue   37 ILE
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain W residue   37 ILE
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  146 MET
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   54 LYS
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   85 ILE
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  105 VAL
Chi-restraints excluded: chain X residue  146 MET
Chi-restraints excluded: chain X residue  211 LYS
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   67 LYS
Chi-restraints excluded: chain Y residue   80 ASP
Chi-restraints excluded: chain Y residue   85 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  174 THR
Chi-restraints excluded: chain Y residue  192 LEU
Chi-restraints excluded: chain Z residue   37 ILE
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  201 LEU
Chi-restraints excluded: chain Z residue  207 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0470
   chunk 108 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 57 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
V  30 ASN
V 171 HIS
V 241 ASN
V 247 HIS
X  55 GLN
X 171 HIS
X 241 ASN
X 247 HIS
Y 151 GLN
Y 171 HIS
Z  55 GLN
Z 241 ASN
Z 247 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.108133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.095560 restraints weight = 20286.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.28
r_work: 0.3389 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9920  Z= 0.210
  Angle     :  0.607   7.728  13425  Z= 0.306
  Chirality :  0.043   0.222   1430
  Planarity :  0.005   0.047   1705
  Dihedral  :  4.889  57.643   1304
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.35 %
    Favored  : 99.57 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 22.61 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1155
  helix:  0.66 (0.22), residues: 540
  sheet: -0.36 (0.26), residues: 330
  loop : -0.32 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP X 156 
 HIS   0.006   0.001   HIS W  15 
 PHE   0.014   0.001   PHE Z 195 
 TYR   0.018   0.002   TYR Y 157 
 ARG   0.009   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 315
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
REVERT: V  196 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: W   30 ASN cc_start: 0.8217 (t0) cc_final: 0.7932 (t0)
REVERT: W  129 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8141 (ttp-110)
REVERT: W  176 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7571 (ptp90)
REVERT: W  207 LEU cc_start: 0.8756 (tp) cc_final: 0.8419 (tm)
REVERT: W  210 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8520 (tptp)
REVERT: X  146 MET cc_start: 0.8978 (ptm) cc_final: 0.8690 (ptt)
REVERT: X  193 ASP cc_start: 0.8473 (t0) cc_final: 0.7869 (t0)
REVERT: X  196 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7943 (mt-10)
REVERT: Y  165 ARG cc_start: 0.7503 (ttm170) cc_final: 0.6792 (mtm-85)
REVERT: Y  196 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7506 (mt-10)
REVERT: Z  161 MET cc_start: 0.7259 (mpt) cc_final: 0.6982 (mpt)
REVERT: Z  165 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7184 (mtm110)
REVERT: Z  193 ASP cc_start: 0.8529 (t70) cc_final: 0.8298 (t0)
REVERT: Z  196 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7927 (mt-10)
REVERT: Z  220 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7280 (tm-30)
  outliers start: 51
  outliers final: 25
  residues processed: 343
  average time/residue: 1.3541
  time to fit residues: 497.0699
Evaluate side-chains
  320 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 293
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   14 LEU
Chi-restraints excluded: chain V residue   54 LYS
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain V residue  211 LYS
Chi-restraints excluded: chain V residue  212 LEU
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  210 LYS
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   54 LYS
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  105 VAL
Chi-restraints excluded: chain X residue  211 LYS
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   85 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Z residue   37 ILE
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  212 LEU
Chi-restraints excluded: chain Z residue  220 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
V  30 ASN
V 241 ASN
V 247 HIS
W  83 HIS
X  83 HIS
X 241 ASN
X 247 HIS
** Z  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  30 ASN
Z 241 ASN
Z 247 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.103663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.090980 restraints weight = 20418.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.24
r_work: 0.3316 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.049   9920  Z= 0.556
  Angle     :  0.734   8.381  13425  Z= 0.375
  Chirality :  0.047   0.262   1430
  Planarity :  0.005   0.048   1705
  Dihedral  :  4.842  20.659   1300
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.43 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 23.96 %
    Favored  : 69.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1155
  helix:  0.46 (0.22), residues: 545
  sheet: -0.45 (0.27), residues: 310
  loop : -0.02 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP W 197 
 HIS   0.005   0.001   HIS W  58 
 PHE   0.023   0.002   PHE V 143 
 TYR   0.023   0.002   TYR X 104 
 ARG   0.009   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 271
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: V  196 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8170 (mt-10)
REVERT: W   30 ASN cc_start: 0.8310 (t0) cc_final: 0.8071 (t0)
REVERT: W  105 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8691 (p)
REVERT: W  210 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8496 (tptp)
REVERT: X  146 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8844 (ptt)
REVERT: X  196 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8122 (mt-10)
REVERT: X  210 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8501 (tmmm)
REVERT: Y  174 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7106 (p)
REVERT: Z  161 MET cc_start: 0.7383 (mpt) cc_final: 0.7105 (mpt)
REVERT: Z  165 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7135 (mtm110)
REVERT: Z  196 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: Z  220 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7448 (tt0)
  outliers start: 63
  outliers final: 33
  residues processed: 307
  average time/residue: 1.2885
  time to fit residues: 424.5407
Evaluate side-chains
  300 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 261
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   37 ILE
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain V residue  211 LYS
Chi-restraints excluded: chain W residue   21 ASP
Chi-restraints excluded: chain W residue   37 ILE
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  160 SER
Chi-restraints excluded: chain W residue  210 LYS
Chi-restraints excluded: chain W residue  211 LYS
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   54 LYS
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  105 VAL
Chi-restraints excluded: chain X residue  146 MET
Chi-restraints excluded: chain X residue  210 LYS
Chi-restraints excluded: chain X residue  211 LYS
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   80 ASP
Chi-restraints excluded: chain Y residue   85 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  165 ARG
Chi-restraints excluded: chain Y residue  174 THR
Chi-restraints excluded: chain Y residue  192 LEU
Chi-restraints excluded: chain Z residue   37 ILE
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue   85 ILE
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  192 LEU
Chi-restraints excluded: chain Z residue  201 LEU
Chi-restraints excluded: chain Z residue  212 LEU
Chi-restraints excluded: chain Z residue  220 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 35 optimal weight:    0.3980
   chunk 80 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 58 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:
V  30 ASN
V 247 HIS
W  55 GLN
X  55 GLN
Z  30 ASN
Z  55 GLN
Z 241 ASN
Z 247 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.107350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.094899 restraints weight = 20512.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.28
r_work: 0.3388 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9920  Z= 0.214
  Angle     :  0.630  10.534  13425  Z= 0.317
  Chirality :  0.043   0.233   1430
  Planarity :  0.005   0.048   1705
  Dihedral  :  4.614  21.254   1300
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.17 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 25.70 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.24), residues: 1155
  helix:  0.52 (0.22), residues: 540
  sheet: -0.47 (0.26), residues: 310
  loop :  0.20 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP X 156 
 HIS   0.005   0.001   HIS Z 247 
 PHE   0.013   0.001   PHE X  17 
 TYR   0.014   0.001   TYR X 178 
 ARG   0.010   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 294
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: V  109 GLU cc_start: 0.7550 (pt0) cc_final: 0.7233 (pt0)
REVERT: V  196 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8077 (mt-10)
REVERT: W   30 ASN cc_start: 0.8176 (t0) cc_final: 0.7908 (t0)
REVERT: W  102 TYR cc_start: 0.8314 (t80) cc_final: 0.7981 (t80)
REVERT: W  140 TYR cc_start: 0.8961 (m-80) cc_final: 0.8634 (m-80)
REVERT: W  165 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7251 (mtm110)
REVERT: W  207 LEU cc_start: 0.8816 (tp) cc_final: 0.8543 (tm)
REVERT: W  210 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8526 (tptp)
REVERT: X  146 MET cc_start: 0.8972 (ptm) cc_final: 0.8692 (ptt)
REVERT: X  196 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7911 (mt-10)
REVERT: X  210 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8946 (tttm)
REVERT: Y  161 MET cc_start: 0.7074 (mpt) cc_final: 0.6763 (mpt)
REVERT: Y  165 ARG cc_start: 0.7630 (ttm170) cc_final: 0.6893 (mtm-85)
REVERT: Y  174 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7032 (p)
REVERT: Y  196 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7810 (mt-10)
REVERT: Z   30 ASN cc_start: 0.8274 (t0) cc_final: 0.7985 (t0)
REVERT: Z  161 MET cc_start: 0.7235 (mpt) cc_final: 0.6969 (mpt)
REVERT: Z  165 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7174 (mtm110)
REVERT: Z  220 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7373 (tm-30)
  outliers start: 53
  outliers final: 33
  residues processed: 328
  average time/residue: 1.1873
  time to fit residues: 417.2549
Evaluate side-chains
  316 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 279
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   54 LYS
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain V residue  221 VAL
Chi-restraints excluded: chain W residue   14 LEU
Chi-restraints excluded: chain W residue   21 ASP
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  210 LYS
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   54 LYS
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   85 ILE
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain X residue  210 LYS
Chi-restraints excluded: chain X residue  221 VAL
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   85 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  160 SER
Chi-restraints excluded: chain Y residue  174 THR
Chi-restraints excluded: chain Y residue  192 LEU
Chi-restraints excluded: chain Y residue  221 VAL
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue   85 ILE
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  201 LEU
Chi-restraints excluded: chain Z residue  211 LYS
Chi-restraints excluded: chain Z residue  212 LEU
Chi-restraints excluded: chain Z residue  220 GLU
Chi-restraints excluded: chain Z residue  221 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0870
   chunk 101 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    1.3564

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

Flipped N/Q/H residues before XYZ refinement:
V 247 HIS
X 241 ASN
** Z  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 247 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.106487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.093864 restraints weight = 20693.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.30
r_work: 0.3368 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9920  Z= 0.303
  Angle     :  0.671  10.308  13425  Z= 0.334
  Chirality :  0.044   0.213   1430
  Planarity :  0.005   0.048   1705
  Dihedral  :  4.645  21.584   1300
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 26.86 %
    Favored  : 67.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1155
  helix:  0.56 (0.22), residues: 545
  sheet: -0.58 (0.26), residues: 310
  loop :  0.19 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP Z 197 
 HIS   0.004   0.001   HIS Y  15 
 PHE   0.015   0.002   PHE V 143 
 TYR   0.018   0.002   TYR Z 157 
 ARG   0.011   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 279
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: V  109 GLU cc_start: 0.7636 (pt0) cc_final: 0.7273 (pt0)
REVERT: W   30 ASN cc_start: 0.8240 (t0) cc_final: 0.7998 (t0)
REVERT: W  102 TYR cc_start: 0.8332 (t80) cc_final: 0.8019 (t80)
REVERT: W  105 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8494 (p)
REVERT: W  165 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7281 (mtm110)
REVERT: W  176 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7299 (ptp90)
REVERT: W  207 LEU cc_start: 0.8816 (tp) cc_final: 0.8521 (tm)
REVERT: W  210 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8486 (tptp)
REVERT: X  146 MET cc_start: 0.9010 (ptm) cc_final: 0.8775 (ptt)
REVERT: X  210 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8456 (tmmm)
REVERT: Y  128 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7851 (mtt-85)
REVERT: Y  129 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7906 (ttp80)
REVERT: Y  147 ASP cc_start: 0.8369 (t0) cc_final: 0.7839 (t70)
REVERT: Y  161 MET cc_start: 0.7128 (mpt) cc_final: 0.6806 (mpt)
REVERT: Y  165 ARG cc_start: 0.7628 (ttm170) cc_final: 0.6869 (mtm-85)
REVERT: Y  174 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7060 (p)
REVERT: Z  161 MET cc_start: 0.7282 (mpt) cc_final: 0.7004 (mpt)
REVERT: Z  165 ARG cc_start: 0.7422 (ttm-80) cc_final: 0.7127 (mtm110)
REVERT: Z  176 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7763 (ptp90)
REVERT: Z  220 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7280 (tm-30)
  outliers start: 58
  outliers final: 41
  residues processed: 316
  average time/residue: 1.1572
  time to fit residues: 391.7390
Evaluate side-chains
  325 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 279
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   14 LEU
Chi-restraints excluded: chain V residue   37 ILE
Chi-restraints excluded: chain V residue   54 LYS
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain V residue  211 LYS
Chi-restraints excluded: chain V residue  221 VAL
Chi-restraints excluded: chain W residue   14 LEU
Chi-restraints excluded: chain W residue   21 ASP
Chi-restraints excluded: chain W residue   37 ILE
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  201 LEU
Chi-restraints excluded: chain W residue  210 LYS
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   54 LYS
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   85 ILE
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  105 VAL
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain X residue  210 LYS
Chi-restraints excluded: chain X residue  221 VAL
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   85 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  160 SER
Chi-restraints excluded: chain Y residue  174 THR
Chi-restraints excluded: chain Y residue  184 GLN
Chi-restraints excluded: chain Y residue  192 LEU
Chi-restraints excluded: chain Y residue  212 LEU
Chi-restraints excluded: chain Y residue  221 VAL
Chi-restraints excluded: chain Z residue   37 ILE
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue   85 ILE
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  184 GLN
Chi-restraints excluded: chain Z residue  201 LEU
Chi-restraints excluded: chain Z residue  212 LEU
Chi-restraints excluded: chain Z residue  220 GLU
Chi-restraints excluded: chain Z residue  221 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
V  30 ASN
V 241 ASN
V 247 HIS
W  55 GLN
X 241 ASN
Z  30 ASN
Z  55 GLN
Z 247 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.107602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.094819 restraints weight = 20860.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.33
r_work: 0.3379 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.4420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9920  Z= 0.255
  Angle     :  0.665   9.640  13425  Z= 0.332
  Chirality :  0.045   0.255   1430
  Planarity :  0.005   0.051   1705
  Dihedral  :  4.620  21.338   1300
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 28.50 %
    Favored  : 66.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.24), residues: 1155
  helix:  0.59 (0.22), residues: 545
  sheet: -0.69 (0.25), residues: 320
  loop :  0.40 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP W 197 
 HIS   0.004   0.001   HIS Z 247 
 PHE   0.015   0.002   PHE Z  17 
 TYR   0.015   0.002   TYR V 157 
 ARG   0.012   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 290
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V  109 GLU cc_start: 0.7568 (pt0) cc_final: 0.7316 (pt0)
REVERT: V  128 ARG cc_start: 0.8400 (mmt-90) cc_final: 0.8075 (mmt-90)
REVERT: W   30 ASN cc_start: 0.8237 (t0) cc_final: 0.8004 (t0)
REVERT: W  102 TYR cc_start: 0.8314 (t80) cc_final: 0.8027 (t80)
REVERT: W  105 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8503 (p)
REVERT: W  165 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7223 (mtm110)
REVERT: W  176 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7290 (ptp90)
REVERT: W  207 LEU cc_start: 0.8794 (tp) cc_final: 0.8407 (tm)
REVERT: W  210 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8541 (tptp)
REVERT: X  128 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.8007 (mmt-90)
REVERT: X  196 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8098 (mt-10)
REVERT: X  210 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8475 (tmmm)
REVERT: Y  128 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7886 (mtt-85)
REVERT: Y  129 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7915 (ttp80)
REVERT: Y  157 TYR cc_start: 0.7662 (m-80) cc_final: 0.7358 (m-80)
REVERT: Y  161 MET cc_start: 0.7073 (mpt) cc_final: 0.6755 (mpt)
REVERT: Y  165 ARG cc_start: 0.7654 (ttm170) cc_final: 0.7000 (mtm-85)
REVERT: Y  174 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7043 (p)
REVERT: Z   30 ASN cc_start: 0.8295 (t0) cc_final: 0.8012 (t0)
REVERT: Z  130 ARG cc_start: 0.7440 (ttp80) cc_final: 0.7162 (ttt180)
REVERT: Z  161 MET cc_start: 0.7293 (mpt) cc_final: 0.7008 (mpt)
REVERT: Z  165 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7150 (mtm110)
REVERT: Z  176 ARG cc_start: 0.8358 (mtp85) cc_final: 0.7764 (ptp90)
  outliers start: 56
  outliers final: 35
  residues processed: 326
  average time/residue: 1.1661
  time to fit residues: 407.3489
Evaluate side-chains
  314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 275
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   37 ILE
Chi-restraints excluded: chain V residue   54 LYS
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain V residue  211 LYS
Chi-restraints excluded: chain V residue  221 VAL
Chi-restraints excluded: chain W residue   21 ASP
Chi-restraints excluded: chain W residue   37 ILE
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  160 SER
Chi-restraints excluded: chain W residue  210 LYS
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   54 LYS
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   85 ILE
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  105 VAL
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain X residue  210 LYS
Chi-restraints excluded: chain X residue  221 VAL
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   85 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  174 THR
Chi-restraints excluded: chain Y residue  192 LEU
Chi-restraints excluded: chain Y residue  212 LEU
Chi-restraints excluded: chain Y residue  221 VAL
Chi-restraints excluded: chain Z residue   23 SER
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue   85 ILE
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  201 LEU
Chi-restraints excluded: chain Z residue  221 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 108 optimal weight:    0.0020
   chunk 100 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
V 241 ASN
V 247 HIS
X  55 GLN
X 241 ASN
Y 241 ASN
Z 247 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.109142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.097108 restraints weight = 20751.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.20
r_work: 0.3420 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9920  Z= 0.208
  Angle     :  0.665  10.014  13425  Z= 0.333
  Chirality :  0.044   0.194   1430
  Planarity :  0.005   0.065   1705
  Dihedral  :  4.556  20.972   1300
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 29.57 %
    Favored  : 65.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.24), residues: 1155
  helix:  0.61 (0.22), residues: 540
  sheet: -0.46 (0.25), residues: 310
  loop :  0.34 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP W 197 
 HIS   0.004   0.001   HIS Z 247 
 PHE   0.018   0.002   PHE Z  17 
 TYR   0.016   0.001   TYR Z 157 
 ARG   0.012   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 295
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: V  109 GLU cc_start: 0.7573 (pt0) cc_final: 0.7311 (pt0)
REVERT: V  128 ARG cc_start: 0.8411 (mmt-90) cc_final: 0.8158 (mmt-90)
REVERT: W   30 ASN cc_start: 0.8240 (t0) cc_final: 0.8011 (t0)
REVERT: W   45 ASP cc_start: 0.8386 (t0) cc_final: 0.8090 (m-30)
REVERT: W  102 TYR cc_start: 0.8268 (t80) cc_final: 0.8012 (t80)
REVERT: W  105 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8413 (p)
REVERT: W  130 ARG cc_start: 0.7542 (ttt180) cc_final: 0.7299 (ttt180)
REVERT: W  137 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8618 (mmtm)
REVERT: W  165 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7198 (mtm110)
REVERT: W  176 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7281 (ptp90)
REVERT: W  207 LEU cc_start: 0.8767 (tp) cc_final: 0.8338 (tm)
REVERT: X  128 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.8130 (mmt-90)
REVERT: X  129 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.7785 (mmm-85)
REVERT: Y  129 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7862 (ttp80)
REVERT: Y  158 MET cc_start: 0.7789 (mmm) cc_final: 0.7309 (mmm)
REVERT: Y  161 MET cc_start: 0.7124 (mpt) cc_final: 0.6787 (mpt)
REVERT: Y  165 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7162 (mtm110)
REVERT: Y  174 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.6974 (p)
REVERT: Y  196 GLU cc_start: 0.8418 (pt0) cc_final: 0.8050 (pm20)
REVERT: Z  130 ARG cc_start: 0.7383 (ttp80) cc_final: 0.6970 (ttt180)
REVERT: Z  161 MET cc_start: 0.7215 (mpt) cc_final: 0.6934 (mpt)
REVERT: Z  165 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7208 (mtt-85)
REVERT: Z  176 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7741 (ptp90)
REVERT: Z  193 ASP cc_start: 0.8499 (t0) cc_final: 0.8196 (m-30)
  outliers start: 50
  outliers final: 33
  residues processed: 327
  average time/residue: 1.1336
  time to fit residues: 397.9073
Evaluate side-chains
  314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 279
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   37 ILE
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain V residue  205 ASP
Chi-restraints excluded: chain V residue  221 VAL
Chi-restraints excluded: chain W residue   21 ASP
Chi-restraints excluded: chain W residue   37 ILE
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  160 SER
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  105 VAL
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain X residue  221 VAL
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  160 SER
Chi-restraints excluded: chain Y residue  174 THR
Chi-restraints excluded: chain Y residue  184 GLN
Chi-restraints excluded: chain Y residue  212 LEU
Chi-restraints excluded: chain Y residue  221 VAL
Chi-restraints excluded: chain Z residue   23 SER
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue   85 ILE
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  201 LEU
Chi-restraints excluded: chain Z residue  221 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
V  30 ASN
V 151 GLN
V 241 ASN
W  55 GLN
X 241 ASN
Z  15 HIS
Z  30 ASN
Z 241 ASN
Z 247 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.109394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.096759 restraints weight = 20895.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.32
r_work: 0.3408 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9920  Z= 0.223
  Angle     :  0.700   9.594  13425  Z= 0.348
  Chirality :  0.044   0.193   1430
  Planarity :  0.005   0.059   1705
  Dihedral  :  4.579  25.135   1300
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 31.69 %
    Favored  : 64.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.24), residues: 1155
  helix:  0.69 (0.22), residues: 545
  sheet: -0.39 (0.26), residues: 310
  loop :  0.35 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP W 197 
 HIS   0.004   0.001   HIS Z 247 
 PHE   0.020   0.002   PHE Z  17 
 TYR   0.029   0.001   TYR V 144 
 ARG   0.013   0.001   ARG V 165 

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 286
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V  128 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.8148 (mmt-90)
REVERT: V  193 ASP cc_start: 0.8475 (t0) cc_final: 0.8268 (m-30)
REVERT: W   30 ASN cc_start: 0.8223 (t0) cc_final: 0.7997 (t0)
REVERT: W  105 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8442 (p)
REVERT: W  130 ARG cc_start: 0.7597 (ttt180) cc_final: 0.7260 (ttt180)
REVERT: W  137 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8623 (mmtm)
REVERT: W  158 MET cc_start: 0.7948 (mmm) cc_final: 0.7586 (mmm)
REVERT: W  165 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.7215 (mtm110)
REVERT: W  176 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7293 (ptp90)
REVERT: W  207 LEU cc_start: 0.8785 (tp) cc_final: 0.8339 (tm)
REVERT: X  128 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.8129 (mmt-90)
REVERT: X  129 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7757 (mmm-85)
REVERT: X  130 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7672 (ttt180)
REVERT: Y  105 VAL cc_start: 0.8958 (t) cc_final: 0.8563 (p)
REVERT: Y  129 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7929 (ttp80)
REVERT: Y  158 MET cc_start: 0.7780 (mmm) cc_final: 0.7344 (mmm)
REVERT: Y  161 MET cc_start: 0.7137 (mpt) cc_final: 0.6792 (mpt)
REVERT: Y  165 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7170 (mtm110)
REVERT: Y  174 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.6934 (p)
REVERT: Z   30 ASN cc_start: 0.8333 (t0) cc_final: 0.8063 (t0)
REVERT: Z  130 ARG cc_start: 0.7435 (ttp80) cc_final: 0.6964 (ttt180)
REVERT: Z  161 MET cc_start: 0.7235 (mpt) cc_final: 0.6860 (mpt)
REVERT: Z  165 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.7126 (mtt-85)
REVERT: Z  176 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7708 (ptp90)
REVERT: Z  193 ASP cc_start: 0.8452 (t0) cc_final: 0.8169 (m-30)
  outliers start: 39
  outliers final: 34
  residues processed: 316
  average time/residue: 1.1497
  time to fit residues: 389.7644
Evaluate side-chains
  315 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 279
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   37 ILE
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  169 ARG
Chi-restraints excluded: chain V residue  190 VAL
Chi-restraints excluded: chain V residue  221 VAL
Chi-restraints excluded: chain W residue   21 ASP
Chi-restraints excluded: chain W residue   37 ILE
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  105 VAL
Chi-restraints excluded: chain W residue  124 ILE
Chi-restraints excluded: chain W residue  160 SER
Chi-restraints excluded: chain W residue  235 THR
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  105 VAL
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain X residue  205 ASP
Chi-restraints excluded: chain X residue  221 VAL
Chi-restraints excluded: chain X residue  239 MET
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   23 SER
Chi-restraints excluded: chain Y residue   37 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  160 SER
Chi-restraints excluded: chain Y residue  174 THR
Chi-restraints excluded: chain Y residue  184 GLN
Chi-restraints excluded: chain Y residue  212 LEU
Chi-restraints excluded: chain Y residue  221 VAL
Chi-restraints excluded: chain Z residue   23 SER
Chi-restraints excluded: chain Z residue   54 LYS
Chi-restraints excluded: chain Z residue   85 ILE
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  201 LEU
Chi-restraints excluded: chain Z residue  211 LYS
Chi-restraints excluded: chain Z residue  221 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 62 optimal weight:    0.0870
   chunk 84 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
V  30 ASN
V 241 ASN
X 241 ASN
Z  15 HIS
Z 241 ASN
Z 247 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.107679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.094563 restraints weight = 20316.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.32
r_work: 0.3365 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9920  Z= 0.339
  Angle     :  0.730   9.182  13425  Z= 0.367
  Chirality :  0.046   0.199   1430
  Planarity :  0.005   0.059   1705
  Dihedral  :  4.747  31.113   1300
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.17 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 31.21 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.24), residues: 1155
  helix:  0.62 (0.22), residues: 545
  sheet: -0.67 (0.26), residues: 320
  loop :  0.48 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP W 197 
 HIS   0.004   0.001   HIS Z 247 
 PHE   0.021   0.002   PHE Z  17 
 TYR   0.037   0.002   TYR V 144 
 ARG   0.013   0.001   ARG V 165 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9247.76 seconds
wall clock time: 159 minutes 45.85 seconds (9585.85 seconds total)