Starting phenix.real_space_refine
on Fri Mar 14 03:21:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vsa_21373/03_2025/6vsa_21373.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vsa_21373/03_2025/6vsa_21373.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vsa_21373/03_2025/6vsa_21373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vsa_21373/03_2025/6vsa_21373.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vsa_21373/03_2025/6vsa_21373.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vsa_21373/03_2025/6vsa_21373.cif"
  }
  resolution = 2.32
  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=   0.020 sd=   0.129
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    1822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 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: 9712
  Number of models: 1
  Model: ""
    Number of chains: 10
    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
    Chain: "V"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "W"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
    Chain: "X"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "Y"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "Z"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 6.50, per 1000 atoms: 0.67
  Number of scatterers: 9712
  At special positions: 0
  Unit cell: (97.2, 99.36, 76.32, 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    1822      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: 2.69
  Conformation dependent library (CDL) restraints added in 1.7 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: 1.21
  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: 3.534A  pdb=" N   ALA V 170 " --> pdb=" O   GLU V 166 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR V 178 " --> pdb=" O   THR V 174 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 206 through 217
      removed outlier: 3.804A  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: 3.537A  pdb=" N   ALA W 170 " --> pdb=" O   GLU W 166 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR W 178 " --> pdb=" O   THR W 174 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 206 through 217
      removed outlier: 3.806A  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: 3.537A  pdb=" N   ALA X 170 " --> pdb=" O   GLU X 166 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR X 178 " --> pdb=" O   THR X 174 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 206 through 217
      removed outlier: 3.808A  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: 5.975A  pdb=" N   ARG Y 130 " --> pdb=" O   GLU Y 126 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 160 through 178
      removed outlier: 3.533A  pdb=" N   ALA Y 170 " --> pdb=" O   GLU Y 166 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   TYR Y 178 " --> pdb=" O   THR Y 174 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 206 through 217
      removed outlier: 3.807A  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: 3.537A  pdb=" N   ALA Z 170 " --> pdb=" O   GLU Z 166 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR Z 178 " --> pdb=" O   THR Z 174 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 206 through 217
      removed outlier: 3.804A  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: 4.169A  pdb=" N   TRP V  11 " --> pdb=" O   VAL V 108 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   THR V  19 " --> pdb=" O   PRO V 100 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLU V 109 " --> pdb=" O   ILE V 186 " (cutoff:3.500A)
      removed outlier: 5.519A  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: 5.929A  pdb=" N   ASP W   9 " --> pdb=" O   LEU W 110 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   LEU W 110 " --> pdb=" O   ASP W   9 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   TRP W  11 " --> pdb=" O   VAL W 108 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   THR W  19 " --> pdb=" O   PRO W 100 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU W 109 " --> pdb=" O   ILE W 186 " (cutoff:3.500A)
      removed outlier: 5.516A  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: 5.945A  pdb=" N   ASP X   9 " --> pdb=" O   LEU X 110 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   LEU X 110 " --> pdb=" O   ASP X   9 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   TRP X  11 " --> pdb=" O   VAL X 108 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   THR X  19 " --> pdb=" O   PRO X 100 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLU X 109 " --> pdb=" O   ILE X 186 " (cutoff:3.500A)
      removed outlier: 5.522A  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: 5.950A  pdb=" N   ASP Y   9 " --> pdb=" O   LEU Y 110 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   LEU Y 110 " --> pdb=" O   ASP Y   9 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   TRP Y  11 " --> pdb=" O   VAL Y 108 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   THR Y  19 " --> pdb=" O   PRO Y 100 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU Y 109 " --> pdb=" O   ILE Y 186 " (cutoff:3.500A)
      removed outlier: 5.512A  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: 5.947A  pdb=" N   ASP Z   9 " --> pdb=" O   LEU Z 110 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   LEU Z 110 " --> pdb=" O   ASP Z   9 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   TRP Z  11 " --> pdb=" O   VAL Z 108 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   THR Z  19 " --> pdb=" O   PRO Z 100 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU Z 109 " --> pdb=" O   ILE Z 186 " (cutoff:3.500A)
      removed outlier: 5.516A  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

    569 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.09

  Time building geometry restraints manager: 3.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2519
        1.33 -     1.46: 3125
        1.46 -     1.59: 4186
        1.59 -     1.73: 0
        1.73 -     1.86: 90
  Bond restraints: 9920
  Sorted by residual:
  bond pdb=" CA  SER W 230 "
       pdb=" CB  SER W 230 "
    ideal  model  delta    sigma   weight residual
    1.529  1.435  0.094 1.58e-02 4.01e+03 3.57e+01
  bond pdb=" CA  SER X 230 "
       pdb=" CB  SER X 230 "
    ideal  model  delta    sigma   weight residual
    1.529  1.436  0.093 1.58e-02 4.01e+03 3.45e+01
  bond pdb=" CA  SER Z 230 "
       pdb=" CB  SER Z 230 "
    ideal  model  delta    sigma   weight residual
    1.529  1.436  0.093 1.58e-02 4.01e+03 3.44e+01
  bond pdb=" CA  SER Y 230 "
       pdb=" CB  SER Y 230 "
    ideal  model  delta    sigma   weight residual
    1.529  1.438  0.092 1.58e-02 4.01e+03 3.36e+01
  bond pdb=" CA  SER V 230 "
       pdb=" CB  SER V 230 "
    ideal  model  delta    sigma   weight residual
    1.529  1.439  0.090 1.58e-02 4.01e+03 3.25e+01
  ... (remaining 9915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 12233
        3.82 -     7.63: 1087
        7.63 -    11.45: 95
       11.45 -    15.27: 9
       15.27 -    19.09: 1
  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   99.12   12.88 1.40e+00 5.10e-01 8.47e+01
  angle pdb=" CB  GLU W  31 "
        pdb=" CG  GLU W  31 "
        pdb=" CD  GLU W  31 "
      ideal   model   delta    sigma   weight residual
     112.60  127.26  -14.66 1.70e+00 3.46e-01 7.43e+01
  angle pdb=" CB  ARG Z 169 "
        pdb=" CG  ARG Z 169 "
        pdb=" CD  ARG Z 169 "
      ideal   model   delta    sigma   weight residual
     111.30  130.39  -19.09 2.30e+00 1.89e-01 6.89e+01
  angle pdb=" CA  THR Y  19 "
        pdb=" CB  THR Y  19 "
        pdb=" OG1 THR Y  19 "
      ideal   model   delta    sigma   weight residual
     109.60   98.34   11.26 1.50e+00 4.44e-01 5.63e+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   97.79   14.21 2.20e+00 2.07e-01 4.17e+01
  ... (remaining 13420 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.08: 5006
       18.08 -    36.15: 617
       36.15 -    54.23: 175
       54.23 -    72.31: 33
       72.31 -    90.38: 19
  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 -103.03  -19.57     0      2.50e+00 1.60e-01 6.13e+01
  dihedral pdb=" N   MET Z 146 "
           pdb=" C   MET Z 146 "
           pdb=" CA  MET Z 146 "
           pdb=" CB  MET Z 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  104.77   18.03     0      2.50e+00 1.60e-01 5.20e+01
  dihedral pdb=" C   CYS X 142 "
           pdb=" N   CYS X 142 "
           pdb=" CA  CYS X 142 "
           pdb=" CB  CYS X 142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.68  -15.92     0      2.50e+00 1.60e-01 4.05e+01
  ... (remaining 5847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.555: 1428
       0.555 -    1.111: 1
       1.111 -    1.666: 0
       1.666 -    2.221: 0
       2.221 -    2.777: 1
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" CB  VAL Y 127 "
            pdb=" CA  VAL Y 127 "
            pdb=" CG1 VAL Y 127 "
            pdb=" CG2 VAL Y 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63    0.15   -2.78 2.00e-01 2.50e+01 1.93e+02
  chirality pdb=" CA  GLU W  31 "
            pdb=" N   GLU W  31 "
            pdb=" C   GLU W  31 "
            pdb=" CB  GLU W  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.90e+00
  chirality pdb=" CA  MET Z 146 "
            pdb=" N   MET Z 146 "
            pdb=" C   MET Z 146 "
            pdb=" CB  MET Z 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.03   -0.51 2.00e-01 2.50e+01 6.63e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR Y 178 "   -0.040 2.00e-02 2.50e+03   8.18e-02 6.70e+01
        pdb=" C   TYR Y 178 "    0.142 2.00e-02 2.50e+03
        pdb=" O   TYR Y 178 "   -0.053 2.00e-02 2.50e+03
        pdb=" N   ALA Y 179 "   -0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE Z 225 "    0.012 2.00e-02 2.50e+03   4.14e-02 3.00e+01
        pdb=" CG  PHE Z 225 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE Z 225 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE Z 225 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE1 PHE Z 225 "   -0.057 2.00e-02 2.50e+03
        pdb=" CE2 PHE Z 225 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  PHE Z 225 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE V 225 "    0.011 2.00e-02 2.50e+03   4.12e-02 2.96e+01
        pdb=" CG  PHE V 225 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE V 225 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE V 225 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 PHE V 225 "   -0.057 2.00e-02 2.50e+03
        pdb=" CE2 PHE V 225 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  PHE V 225 "    0.078 2.00e-02 2.50e+03
  ... (remaining 1702 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 245
        2.62 -     3.19: 8760
        3.19 -     3.76: 17303
        3.76 -     4.33: 25745
        4.33 -     4.90: 39699
  Nonbonded interactions: 91752
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS W  67 "
            pdb=" OD1 ASP Y 194 "
     model   vdw
     2.048 3.120
  nonbonded pdb=" NZ  LYS X  67 "
            pdb=" OD1 ASP Z 194 "
     model   vdw
     2.054 3.120
  nonbonded pdb=" OD1 ASP X 194 "
            pdb=" NZ  LYS Y  67 "
     model   vdw
     2.066 3.120
  nonbonded pdb=" OD1 ASP V 194 "
            pdb=" NZ  LYS Z  67 "
     model   vdw
     2.073 3.120
  nonbonded pdb=" O   GLY Y  65 "
            pdb=" O   HOH Y 301 "
     model   vdw
     2.073 3.040
  ... (remaining 91747 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain '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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.120
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.110
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.040
  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:30.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9221
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      :  0.013   0.115   9920  Z= 0.861
  Angle     :  2.263  19.087  13425  Z= 1.465
  Chirality :  0.159   2.777   1430
  Planarity :  0.012   0.082   1705
  Dihedral  : 18.035  90.385   3630
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 13.04 %
    Favored  : 82.51 %
  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: -1.58 (0.22), residues: 1155
  helix: -1.92 (0.19), residues: 505
  sheet:  0.61 (0.28), residues: 315
  loop : -0.88 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.014   TRP W  25 
 HIS   0.030   0.008   HIS W  15 
 PHE   0.079   0.014   PHE Z 225 
 TYR   0.049   0.011   TYR X 157 
 ARG   0.038   0.004   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
  147 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 101
  time to evaluate  : 1.228 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6902 (tp40)
REVERT: W    6 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7073 (tp40)
REVERT: X    6 GLN cc_start: 0.7057 (mp-120) cc_final: 0.6486 (tp40)
REVERT: Y    6 GLN cc_start: 0.6896 (mp10) cc_final: 0.6242 (tp40)
REVERT: Y  161 MET cc_start: 0.8707 (tmt) cc_final: 0.8477 (tmt)
REVERT: Z    6 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6996 (tp40)
  outliers start: 46
  outliers final: 5
  residues processed: 134
  average time/residue: 1.7596
  time to fit residues: 249.8650
Evaluate side-chains
  80 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue    6 GLN
Chi-restraints excluded: chain W residue    6 GLN
Chi-restraints excluded: chain W residue    7 THR
Chi-restraints excluded: chain W residue   31 GLU
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Z residue    6 GLN
Chi-restraints excluded: chain Z residue    7 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
V   6 GLN
W   6 GLN
W  83 HIS
W 163 GLN
** W 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X  83 HIS
Z   6 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.062169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.051316 restraints weight = 34764.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.66
r_work: 0.2998 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9920  Z= 0.204
  Angle     :  0.590   6.891  13425  Z= 0.318
  Chirality :  0.042   0.315   1430
  Planarity :  0.005   0.038   1705
  Dihedral  :  5.825  37.606   1317
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.00 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.39 (0.23), residues: 1155
  helix:  0.06 (0.21), residues: 520
  sheet: -0.36 (0.25), residues: 365
  loop : -0.22 (0.34), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP X 156 
 HIS   0.002   0.001   HIS V  83 
 PHE   0.017   0.002   PHE Y 225 
 TYR   0.019   0.002   TYR Z 157 
 ARG   0.007   0.001   ARG Y 169 

*********************** 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
  125 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 1.202 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7155 (mp10) cc_final: 0.6610 (pp30)
REVERT: W    6 GLN cc_start: 0.7203 (mp10) cc_final: 0.6721 (pp30)
REVERT: X    6 GLN cc_start: 0.7141 (mp-120) cc_final: 0.6346 (tm-30)
REVERT: X  161 MET cc_start: 0.8190 (tmm) cc_final: 0.7747 (tmt)
REVERT: Y    6 GLN cc_start: 0.6730 (mp10) cc_final: 0.6070 (tm-30)
REVERT: Y  161 MET cc_start: 0.8166 (tmt) cc_final: 0.7839 (tmt)
REVERT: Z    6 GLN cc_start: 0.7059 (mp10) cc_final: 0.6232 (tm-30)
REVERT: Z  161 MET cc_start: 0.8233 (tmm) cc_final: 0.7963 (tmt)
REVERT: Z  210 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9172 (tttm)
  outliers start: 25
  outliers final: 11
  residues processed: 123
  average time/residue: 1.3797
  time to fit residues: 181.2996
Evaluate side-chains
  95 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue  110 LEU
Chi-restraints excluded: chain W residue    7 THR
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  110 LEU
Chi-restraints excluded: chain X residue  244 SER
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Z residue    7 THR
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  110 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  210 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 69 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
V 123 GLN
W 241 ASN
X 123 GLN
** X 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 163 GLN
Y 171 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.059536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.048577 restraints weight = 35504.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.66
r_work: 0.2905 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.050   9920  Z= 0.570
  Angle     :  0.645   6.404  13425  Z= 0.345
  Chirality :  0.045   0.400   1430
  Planarity :  0.004   0.034   1705
  Dihedral  :  4.981  25.805   1302
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.09 %
    Favored  : 99.83 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.91 %
    Favored  : 79.90 %
  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:  0.85 (0.24), residues: 1155
  helix:  0.94 (0.22), residues: 490
  sheet:  0.24 (0.28), residues: 310
  loop :  0.64 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP V 197 
 HIS   0.004   0.001   HIS W  58 
 PHE   0.015   0.002   PHE X 143 
 TYR   0.021   0.003   TYR Y 157 
 ARG   0.003   0.001   ARG Z 130 

*********************** 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
  108 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 75
  time to evaluate  : 1.108 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7030 (mp10) cc_final: 0.6560 (pp30)
REVERT: W    6 GLN cc_start: 0.7046 (mp10) cc_final: 0.6540 (pp30)
REVERT: W  210 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9210 (tptm)
REVERT: X    6 GLN cc_start: 0.6993 (mp-120) cc_final: 0.6403 (tp40)
REVERT: Y    6 GLN cc_start: 0.6798 (mp10) cc_final: 0.6161 (tp40)
REVERT: Y  161 MET cc_start: 0.8325 (tmt) cc_final: 0.8051 (tmt)
REVERT: Z    6 GLN cc_start: 0.7118 (mp10) cc_final: 0.6634 (pp30)
REVERT: Z  161 MET cc_start: 0.8458 (tmm) cc_final: 0.8166 (tmt)
  outliers start: 33
  outliers final: 18
  residues processed: 103
  average time/residue: 1.3723
  time to fit residues: 151.1664
Evaluate side-chains
  93 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  151 GLN
Chi-restraints excluded: chain W residue    7 THR
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  210 LYS
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  110 LEU
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain X residue  244 SER
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  230 SER
Chi-restraints excluded: chain Z residue    7 THR
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  110 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  230 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0470
   overall best weight:    1.2086

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

Flipped N/Q/H residues before XYZ refinement:
X 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.061600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.050791 restraints weight = 34823.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.67
r_work: 0.2995 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2867 r_free = 0.2867    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.2819

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= 0.173
  Angle     :  0.484   6.990  13425  Z= 0.256
  Chirality :  0.040   0.303   1430
  Planarity :  0.004   0.036   1705
  Dihedral  :  4.545  18.414   1302
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.35 %
    Favored  : 99.57 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.71 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.47 (0.24), residues: 1155
  helix:  0.85 (0.22), residues: 540
  sheet: -0.19 (0.27), residues: 345
  loop :  0.33 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS Z  83 
 PHE   0.011   0.001   PHE Y 195 
 TYR   0.014   0.001   TYR Z  97 
 ARG   0.004   0.001   ARG X 129 

*********************** 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
  116 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 1.295 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.6973 (mp10) cc_final: 0.6511 (pp30)
REVERT: W    6 GLN cc_start: 0.6995 (mp10) cc_final: 0.6541 (pp30)
REVERT: X    6 GLN cc_start: 0.7025 (mp-120) cc_final: 0.6360 (tp40)
REVERT: X  161 MET cc_start: 0.8166 (tmm) cc_final: 0.7724 (tmt)
REVERT: Y    6 GLN cc_start: 0.6944 (mp10) cc_final: 0.6241 (tp40)
REVERT: Y  161 MET cc_start: 0.8292 (tmt) cc_final: 0.7988 (tmt)
REVERT: Z    6 GLN cc_start: 0.7135 (mp10) cc_final: 0.6599 (pp30)
REVERT: Z  161 MET cc_start: 0.8508 (tmm) cc_final: 0.8039 (tmt)
  outliers start: 34
  outliers final: 10
  residues processed: 107
  average time/residue: 1.7419
  time to fit residues: 199.3075
Evaluate side-chains
  85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  123 GLN
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  110 LEU
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  230 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 80 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
W 163 GLN
X 123 GLN
** X 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.059656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.048779 restraints weight = 35172.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.61
r_work: 0.2921 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8959
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.047   9920  Z= 0.518
  Angle     :  0.601   7.491  13425  Z= 0.318
  Chirality :  0.044   0.369   1430
  Planarity :  0.004   0.035   1705
  Dihedral  :  4.677  19.228   1300
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.61 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.62 %
    Favored  : 80.68 %
  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:  0.87 (0.25), residues: 1155
  helix:  1.25 (0.22), residues: 505
  sheet: -0.44 (0.27), residues: 345
  loop :  1.09 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP V 197 
 HIS   0.004   0.001   HIS W 171 
 PHE   0.012   0.002   PHE Z 143 
 TYR   0.018   0.002   TYR Y 157 
 ARG   0.002   0.000   ARG X 224 

*********************** 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
  98 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 1.140 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7000 (mp10) cc_final: 0.6502 (pp30)
REVERT: W    6 GLN cc_start: 0.6987 (mp10) cc_final: 0.6621 (pp30)
REVERT: X    6 GLN cc_start: 0.7016 (mp-120) cc_final: 0.6387 (tp40)
REVERT: X  137 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9073 (mmtm)
REVERT: X  161 MET cc_start: 0.8419 (tmm) cc_final: 0.8005 (tmt)
REVERT: Y    6 GLN cc_start: 0.6869 (mp10) cc_final: 0.6213 (tp40)
REVERT: Y  161 MET cc_start: 0.8326 (tmt) cc_final: 0.8067 (tmt)
REVERT: Z    6 GLN cc_start: 0.7076 (mp10) cc_final: 0.6634 (pp30)
REVERT: Z  161 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8235 (tmt)
  outliers start: 28
  outliers final: 16
  residues processed: 93
  average time/residue: 1.3803
  time to fit residues: 137.6847
Evaluate side-chains
  87 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   71 LEU
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  151 GLN
Chi-restraints excluded: chain W residue    7 THR
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  110 LEU
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain X residue  137 LYS
Chi-restraints excluded: chain X residue  244 SER
Chi-restraints excluded: chain Y residue    7 THR
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  230 SER
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  161 MET
Chi-restraints excluded: chain Z residue  230 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
W 163 GLN
W 184 GLN
** X 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  15 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.061663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.050861 restraints weight = 35330.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 2.73
r_work: 0.2966 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.2911

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= 0.179
  Angle     :  0.483   8.245  13425  Z= 0.252
  Chirality :  0.040   0.295   1430
  Planarity :  0.004   0.036   1705
  Dihedral  :  4.417  18.225   1300
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.49 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.54 (0.24), residues: 1155
  helix:  1.10 (0.22), residues: 540
  sheet: -0.56 (0.26), residues: 345
  loop :  0.55 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Y 156 
 HIS   0.003   0.001   HIS Z  83 
 PHE   0.010   0.001   PHE X 143 
 TYR   0.014   0.001   TYR Z  97 
 ARG   0.003   0.000   ARG V 149 

*********************** 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
  103 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 1.330 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7004 (mp10) cc_final: 0.6553 (pp30)
REVERT: W    6 GLN cc_start: 0.6979 (mp10) cc_final: 0.6636 (pp30)
REVERT: X    6 GLN cc_start: 0.6978 (mp-120) cc_final: 0.6400 (tp40)
REVERT: Y    6 GLN cc_start: 0.6902 (mp10) cc_final: 0.6258 (tp40)
REVERT: Y  161 MET cc_start: 0.8202 (tmt) cc_final: 0.7934 (tmt)
REVERT: Z    6 GLN cc_start: 0.7112 (mp10) cc_final: 0.6726 (pp30)
REVERT: Z  161 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8121 (tmt)
  outliers start: 26
  outliers final: 11
  residues processed: 95
  average time/residue: 2.3134
  time to fit residues: 235.4879
Evaluate side-chains
  85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 3.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  123 GLN
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  110 LEU
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  230 SER
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  161 MET
Chi-restraints excluded: chain Z residue  230 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 112 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 104 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
V 163 GLN
X 123 GLN
X 163 GLN
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.061955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.051137 restraints weight = 35910.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.75
r_work: 0.2981 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.3058

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= 0.175
  Angle     :  0.462   8.010  13425  Z= 0.242
  Chirality :  0.040   0.325   1430
  Planarity :  0.003   0.036   1705
  Dihedral  :  4.220  17.589   1300
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.87 %
    Favored  : 79.61 %
  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:  0.74 (0.24), residues: 1155
  helix:  1.24 (0.22), residues: 540
  sheet: -0.21 (0.27), residues: 310
  loop :  0.20 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS Z  83 
 PHE   0.009   0.001   PHE X 143 
 TYR   0.013   0.001   TYR Z  97 
 ARG   0.003   0.000   ARG V 149 

*********************** 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
  100 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 1.195 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7147 (mp10) cc_final: 0.6680 (pp30)
REVERT: W    6 GLN cc_start: 0.6954 (mp10) cc_final: 0.6661 (pp30)
REVERT: W   71 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9147 (tp)
REVERT: X    6 GLN cc_start: 0.6994 (mp-120) cc_final: 0.6431 (tp40)
REVERT: X  161 MET cc_start: 0.8102 (tmm) cc_final: 0.7715 (tmt)
REVERT: Y    6 GLN cc_start: 0.7018 (mp10) cc_final: 0.6365 (tp40)
REVERT: Y  161 MET cc_start: 0.8221 (tmt) cc_final: 0.7975 (tmt)
REVERT: Z    6 GLN cc_start: 0.7116 (mp10) cc_final: 0.6744 (pp30)
REVERT: Z  161 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8021 (tmt)
  outliers start: 26
  outliers final: 14
  residues processed: 94
  average time/residue: 1.2884
  time to fit residues: 130.2865
Evaluate side-chains
  87 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   71 LEU
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  123 GLN
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  123 GLN
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  127 VAL
Chi-restraints excluded: chain Y residue  230 SER
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  161 MET
Chi-restraints excluded: chain Z residue  230 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 85 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 91 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 171 HIS
X 123 GLN
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.060565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.049590 restraints weight = 35799.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.75
r_work: 0.2930 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   9920  Z= 0.383
  Angle     :  0.551   8.800  13425  Z= 0.285
  Chirality :  0.042   0.343   1430
  Planarity :  0.004   0.035   1705
  Dihedral  :  4.417  18.049   1300
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.55 %
    Favored  : 79.13 %
  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:  0.65 (0.24), residues: 1155
  helix:  1.18 (0.22), residues: 535
  sheet: -0.36 (0.27), residues: 310
  loop :  0.26 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP Y 156 
 HIS   0.003   0.001   HIS W  58 
 PHE   0.011   0.001   PHE Z 143 
 TYR   0.015   0.002   TYR Y 157 
 ARG   0.002   0.000   ARG Z 224 

*********************** 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
  94 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 1.106 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.6999 (mp10) cc_final: 0.6512 (pp30)
REVERT: W    6 GLN cc_start: 0.6929 (mp10) cc_final: 0.6597 (pp30)
REVERT: W   71 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9221 (tp)
REVERT: X    6 GLN cc_start: 0.6980 (mp-120) cc_final: 0.6465 (tp40)
REVERT: X  161 MET cc_start: 0.8135 (tmm) cc_final: 0.7734 (tmt)
REVERT: Y    6 GLN cc_start: 0.6886 (mp10) cc_final: 0.6278 (tp40)
REVERT: Y  161 MET cc_start: 0.8196 (tmt) cc_final: 0.7953 (tmt)
REVERT: Z    6 GLN cc_start: 0.7002 (mp10) cc_final: 0.6630 (pp30)
REVERT: Z  161 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8084 (tmt)
  outliers start: 24
  outliers final: 14
  residues processed: 90
  average time/residue: 1.2593
  time to fit residues: 122.0315
Evaluate side-chains
  85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   71 LEU
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain V residue  123 GLN
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  123 GLN
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  127 VAL
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  110 LEU
Chi-restraints excluded: chain Z residue  161 MET
Chi-restraints excluded: chain Z residue  230 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 123 GLN
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.061899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.051082 restraints weight = 35347.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.74
r_work: 0.2978 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9920  Z= 0.178
  Angle     :  0.472   8.589  13425  Z= 0.246
  Chirality :  0.040   0.330   1430
  Planarity :  0.003   0.035   1705
  Dihedral  :  4.256  18.000   1300
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.03 %
    Favored  : 79.13 %
  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:  0.68 (0.24), residues: 1155
  helix:  1.21 (0.22), residues: 540
  sheet: -0.33 (0.27), residues: 310
  loop :  0.22 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS V  83 
 PHE   0.009   0.001   PHE Z 195 
 TYR   0.013   0.001   TYR Z  97 
 ARG   0.003   0.000   ARG X 149 

*********************** 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
  91 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 1.222 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7166 (mp10) cc_final: 0.6664 (pp30)
REVERT: W    6 GLN cc_start: 0.6920 (mp10) cc_final: 0.6602 (pp30)
REVERT: W   71 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9187 (tp)
REVERT: X    6 GLN cc_start: 0.6991 (mp-120) cc_final: 0.6451 (tp40)
REVERT: X  161 MET cc_start: 0.8110 (tmm) cc_final: 0.7730 (tmt)
REVERT: Y    6 GLN cc_start: 0.6945 (mp10) cc_final: 0.6351 (tp40)
REVERT: Y  161 MET cc_start: 0.8205 (tmt) cc_final: 0.7958 (tmt)
REVERT: Z    6 GLN cc_start: 0.7056 (mp10) cc_final: 0.6732 (pp30)
REVERT: Z  161 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8055 (tmt)
  outliers start: 19
  outliers final: 12
  residues processed: 87
  average time/residue: 1.2829
  time to fit residues: 120.1769
Evaluate side-chains
  86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   71 LEU
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  127 VAL
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  161 MET
Chi-restraints excluded: chain Z residue  230 SER
Chi-restraints excluded: chain Z residue  239 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** V 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.062166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.051294 restraints weight = 35871.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.78
r_work: 0.2980 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9920  Z= 0.178
  Angle     :  0.483   9.777  13425  Z= 0.248
  Chirality :  0.040   0.329   1430
  Planarity :  0.003   0.035   1705
  Dihedral  :  4.162  17.883   1300
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.23 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.77 (0.24), residues: 1155
  helix:  1.30 (0.22), residues: 540
  sheet: -0.29 (0.27), residues: 310
  loop :  0.25 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS V  83 
 PHE   0.008   0.001   PHE X 195 
 TYR   0.012   0.001   TYR Z  97 
 ARG   0.003   0.000   ARG V 149 

********************** 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
  94 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 1.212 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7129 (mp10) cc_final: 0.6646 (pp30)
REVERT: W    6 GLN cc_start: 0.6899 (mp10) cc_final: 0.6599 (pp30)
REVERT: W   71 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9189 (tp)
REVERT: X    6 GLN cc_start: 0.6984 (mp-120) cc_final: 0.6441 (tp40)
REVERT: X   71 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9265 (tp)
REVERT: X  161 MET cc_start: 0.8105 (tmm) cc_final: 0.7730 (tmt)
REVERT: Y    6 GLN cc_start: 0.6962 (mp10) cc_final: 0.6347 (tp40)
REVERT: Y  161 MET cc_start: 0.8200 (tmt) cc_final: 0.7952 (tmt)
REVERT: Z    6 GLN cc_start: 0.6931 (mp10) cc_final: 0.6583 (pp30)
REVERT: Z  161 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8067 (tmt)
  outliers start: 16
  outliers final: 11
  residues processed: 90
  average time/residue: 1.5825
  time to fit residues: 152.6367
Evaluate side-chains
  84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   71 LEU
Chi-restraints excluded: chain V residue   99 LEU
Chi-restraints excluded: chain W residue   71 LEU
Chi-restraints excluded: chain W residue   85 ILE
Chi-restraints excluded: chain W residue   99 LEU
Chi-restraints excluded: chain W residue  230 SER
Chi-restraints excluded: chain X residue   71 LEU
Chi-restraints excluded: chain X residue   99 LEU
Chi-restraints excluded: chain X residue  124 ILE
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Y residue  127 VAL
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  161 MET
Chi-restraints excluded: chain Z residue  230 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0970
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0030
   chunk 13 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    1.6194

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

Flipped N/Q/H residues before XYZ refinement:
V 163 GLN
X 123 GLN
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.061912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.051009 restraints weight = 35629.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.74
r_work: 0.2982 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2982
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9920  Z= 0.191
  Angle     :  0.477   9.325  13425  Z= 0.247
  Chirality :  0.040   0.329   1430
  Planarity :  0.003   0.035   1705
  Dihedral  :  4.145  17.903   1300
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.17 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 19.32 %
    Favored  : 79.03 %
  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:  0.77 (0.24), residues: 1155
  helix:  1.30 (0.22), residues: 540
  sheet: -0.30 (0.27), residues: 310
  loop :  0.27 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS V  83 
 PHE   0.008   0.001   PHE V 143 
 TYR   0.012   0.001   TYR Z  97 
 ARG   0.003   0.000   ARG V 149 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6979.31 seconds
wall clock time: 124 minutes 24.25 seconds (7464.25 seconds total)