Starting phenix.real_space_refine
on Wed Mar  4 00:25:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vsa_21373/03_2026/6vsa_21373.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vsa_21373/03_2026/6vsa_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_2026/6vsa_21373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vsa_21373/03_2026/6vsa_21373.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vsa_21373/03_2026/6vsa_21373.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vsa_21373/03_2026/6vsa_21373.cif"
  }
  resolution = 2.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.020 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.02, per 1000 atoms: 0.21
  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: 0.67
  Conformation dependent library (CDL) restraints added in 500.0 milliseconds
  

  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: 0.47
  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: 1.74

  Time building geometry restraints manager: 0.92 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: 0.01
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:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.790
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  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:7.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.750
-------------------------------------------------------------------------------
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= 0.875
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (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
 ARG   0.038   0.004   ARG Y 129 
 TYR   0.049   0.011   TYR X 157 
 PHE   0.079   0.014   PHE Z 225 
 TRP   0.040   0.014   TRP W  25 
 HIS   0.030   0.008   HIS W  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.01325 ( 9920)
  covalent geometry    : angle       2.26304 (13425)
  hydrogen bonds       : bond        0.18025 (  569)
  hydrogen bonds       : angle       7.52859 ( 1572)

*********************** 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  : 0.373 
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: 0.7317
  time to fit residues: 103.5815
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  : 0.379 
-------------------------------------------------------------------------------
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 108 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.062066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.051215 restraints weight = 34708.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.66
r_work: 0.2995 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    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 = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
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   0.054   9920  Z= 0.160
  Angle     :  0.586   6.849  13425  Z= 0.316
  Chirality :  0.042   0.305   1430
  Planarity :  0.005   0.039   1705
  Dihedral  :  5.842  37.757   1317
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.10 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.23), residues: 1155
  helix:  0.07 (0.21), residues: 520
  sheet: -0.37 (0.25), residues: 365
  loop : -0.20 (0.34), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Y 169 
 TYR   0.020   0.002   TYR Z 157 
 PHE   0.016   0.002   PHE Y 225 
 TRP   0.022   0.002   TRP X 156 
 HIS   0.002   0.001   HIS V  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9920)
  covalent geometry    : angle       0.58647 (13425)
  hydrogen bonds       : bond        0.04414 (  569)
  hydrogen bonds       : angle       5.60040 ( 1572)

*********************** 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
  123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.262 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7161 (mp10) cc_final: 0.6610 (pp30)
REVERT: W    6 GLN cc_start: 0.7205 (mp10) cc_final: 0.6714 (pp30)
REVERT: X    6 GLN cc_start: 0.7139 (mp-120) cc_final: 0.6348 (tm-30)
REVERT: X  161 MET cc_start: 0.8199 (tmm) cc_final: 0.7814 (tmt)
REVERT: Y    6 GLN cc_start: 0.6697 (mp10) cc_final: 0.6034 (tm-30)
REVERT: Y  161 MET cc_start: 0.8167 (tmt) cc_final: 0.7834 (tmt)
REVERT: Z    6 GLN cc_start: 0.7097 (mp10) cc_final: 0.6252 (tm-30)
REVERT: Z  161 MET cc_start: 0.8244 (tmm) cc_final: 0.7965 (tmt)
REVERT: Z  210 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9174 (tttm)
  outliers start: 25
  outliers final: 11
  residues processed: 120
  average time/residue: 0.6626
  time to fit residues: 84.3698
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  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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    7 THR
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 14 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 110 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    5.5788

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.059428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.048490 restraints weight = 35604.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.66
r_work: 0.2921 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8959
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   9920  Z= 0.350
  Angle     :  0.610   6.510  13425  Z= 0.327
  Chirality :  0.044   0.403   1430
  Planarity :  0.004   0.033   1705
  Dihedral  :  4.951  24.358   1303
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.09 %
    Favored  : 99.83 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.81 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.24), residues: 1155
  helix:  0.68 (0.22), residues: 520
  sheet:  0.22 (0.28), residues: 310
  loop :  0.26 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Y 169 
 TYR   0.020   0.002   TYR Y 157 
 PHE   0.014   0.002   PHE X 143 
 TRP   0.012   0.001   TRP V 197 
 HIS   0.004   0.001   HIS W  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00741 ( 9920)
  covalent geometry    : angle       0.61048 (13425)
  hydrogen bonds       : bond        0.04774 (  569)
  hydrogen bonds       : angle       5.65000 ( 1572)

*********************** 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
  107 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 75
  time to evaluate  : 0.321 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7012 (mp10) cc_final: 0.6538 (pp30)
REVERT: W    6 GLN cc_start: 0.7034 (mp10) cc_final: 0.6534 (pp30)
REVERT: W  210 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9205 (tptm)
REVERT: X    6 GLN cc_start: 0.6994 (mp-120) cc_final: 0.6408 (tp40)
REVERT: Y    6 GLN cc_start: 0.6768 (mp10) cc_final: 0.6120 (tp40)
REVERT: Y  161 MET cc_start: 0.8318 (tmt) cc_final: 0.8029 (tmt)
REVERT: Z    6 GLN cc_start: 0.7125 (mp10) cc_final: 0.6637 (pp30)
REVERT: Z  161 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8148 (tmt)
  outliers start: 32
  outliers final: 18
  residues processed: 103
  average time/residue: 0.6609
  time to fit residues: 72.3310
Evaluate side-chains
  95 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
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  161 MET
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 53 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 77 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:   20.0000
   chunk 66 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
X 123 GLN
X 184 GLN
Z  15 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.061792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.050853 restraints weight = 35740.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.77
r_work: 0.2983 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2982
|-occupancy refinement: start-------------------------------------------------|
| 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 |
|-----------------------------------------------------------------------------|
|-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: 0.8769
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9920  Z= 0.119
  Angle     :  0.478   7.312  13425  Z= 0.252
  Chirality :  0.040   0.302   1430
  Planarity :  0.004   0.035   1705
  Dihedral  :  4.482  18.409   1303
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.35 %
    Favored  : 99.57 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.81 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.24), residues: 1155
  helix:  0.90 (0.22), residues: 540
  sheet: -0.14 (0.27), residues: 345
  loop :  0.36 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG X 130 
 TYR   0.013   0.001   TYR Z  97 
 PHE   0.010   0.001   PHE Y 195 
 TRP   0.015   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS Z  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9920)
  covalent geometry    : angle       0.47796 (13425)
  hydrogen bonds       : bond        0.03540 (  569)
  hydrogen bonds       : angle       5.23119 ( 1572)

*********************** 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
  115 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 0.279 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7096 (mp10) cc_final: 0.6657 (pp30)
REVERT: W    6 GLN cc_start: 0.7070 (mp10) cc_final: 0.6639 (pp30)
REVERT: X    6 GLN cc_start: 0.6994 (mp-120) cc_final: 0.6351 (tp40)
REVERT: X  161 MET cc_start: 0.8082 (tmm) cc_final: 0.7382 (tmt)
REVERT: Y    6 GLN cc_start: 0.6929 (mp10) cc_final: 0.6492 (pp30)
REVERT: Y  161 MET cc_start: 0.8203 (tmt) cc_final: 0.7901 (tmt)
REVERT: Z    6 GLN cc_start: 0.7135 (mp10) cc_final: 0.6646 (pp30)
REVERT: Z  161 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7861 (tmt)
  outliers start: 31
  outliers final: 9
  residues processed: 107
  average time/residue: 0.6228
  time to fit residues: 71.0480
Evaluate side-chains
  87 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   99 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  110 LEU
Chi-restraints excluded: chain Y residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
Chi-restraints excluded: chain Z residue  161 MET
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 20 optimal weight:    3.9990
   chunk 69 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 57 optimal weight:   30.0000
   chunk 56 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    5.1990

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.060497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.049625 restraints weight = 35288.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.64
r_work: 0.2934 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    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 = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   9920  Z= 0.321
  Angle     :  0.578   7.543  13425  Z= 0.305
  Chirality :  0.043   0.348   1430
  Planarity :  0.004   0.036   1705
  Dihedral  :  4.610  18.974   1300
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.52 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.00 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.24), residues: 1155
  helix:  0.98 (0.22), residues: 535
  sheet: -0.40 (0.27), residues: 345
  loop :  0.57 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 129 
 TYR   0.017   0.002   TYR Y 157 
 PHE   0.012   0.002   PHE Y 143 
 TRP   0.009   0.001   TRP Y 156 
 HIS   0.003   0.001   HIS W 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 ( 9920)
  covalent geometry    : angle       0.57777 (13425)
  hydrogen bonds       : bond        0.04324 (  569)
  hydrogen bonds       : angle       5.53614 ( 1572)

*********************** 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
  97 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.358 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.6996 (mp10) cc_final: 0.6509 (pp30)
REVERT: W    6 GLN cc_start: 0.6991 (mp10) cc_final: 0.6599 (pp30)
REVERT: X    6 GLN cc_start: 0.6997 (mp-120) cc_final: 0.6389 (tp40)
REVERT: X  137 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9067 (mmtm)
REVERT: X  161 MET cc_start: 0.8285 (tmm) cc_final: 0.7790 (tmt)
REVERT: Y    6 GLN cc_start: 0.6898 (mp10) cc_final: 0.6260 (tp40)
REVERT: Y  161 MET cc_start: 0.8342 (tmt) cc_final: 0.8067 (tmt)
REVERT: Z    6 GLN cc_start: 0.7073 (mp10) cc_final: 0.6627 (pp30)
REVERT: Z  161 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8147 (tmt)
  outliers start: 26
  outliers final: 15
  residues processed: 94
  average time/residue: 0.6209
  time to fit residues: 62.2101
Evaluate side-chains
  86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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   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   99 LEU
Chi-restraints excluded: chain Y residue  230 SER
Chi-restraints excluded: chain Z residue   99 LEU
Chi-restraints excluded: chain Z residue  160 SER
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 83 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 34 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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
** 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 = 0.3433 r_free = 0.3433 target = 0.061499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.050644 restraints weight = 35547.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.74
r_work: 0.2956 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    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 = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9920  Z= 0.157
  Angle     :  0.494   8.039  13425  Z= 0.259
  Chirality :  0.041   0.369   1430
  Planarity :  0.004   0.036   1705
  Dihedral  :  4.426  18.487   1300
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.24), residues: 1155
  helix:  1.12 (0.22), residues: 540
  sheet: -0.12 (0.27), residues: 310
  loop :  0.21 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Z 169 
 TYR   0.014   0.001   TYR Z  97 
 PHE   0.010   0.001   PHE Y 143 
 TRP   0.012   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS Z  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9920)
  covalent geometry    : angle       0.49423 (13425)
  hydrogen bonds       : bond        0.03580 (  569)
  hydrogen bonds       : angle       5.31904 ( 1572)

*********************** 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: 25
    poor density    : 78
  time to evaluate  : 0.397 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.6997 (mp10) cc_final: 0.6551 (pp30)
REVERT: W    6 GLN cc_start: 0.6934 (mp10) cc_final: 0.6596 (pp30)
REVERT: W   71 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9196 (tp)
REVERT: X    6 GLN cc_start: 0.6985 (mp-120) cc_final: 0.6404 (tp40)
REVERT: X  161 MET cc_start: 0.8167 (tmm) cc_final: 0.7695 (tmt)
REVERT: Y    6 GLN cc_start: 0.6830 (mp10) cc_final: 0.6281 (tp40)
REVERT: Y  161 MET cc_start: 0.8229 (tmt) cc_final: 0.7974 (tmt)
REVERT: Z    6 GLN cc_start: 0.7088 (mp10) cc_final: 0.6725 (pp30)
REVERT: Z  161 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8064 (tmt)
  outliers start: 25
  outliers final: 12
  residues processed: 96
  average time/residue: 0.6114
  time to fit residues: 62.8185
Evaluate side-chains
  88 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  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 51 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 94 optimal weight:    0.8980
   chunk 98 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 59 optimal weight:    9.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
V 163 GLN
W 163 GLN
X 123 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 = 0.3402 r_free = 0.3402 target = 0.060451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.049494 restraints weight = 35613.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.73
r_work: 0.2916 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    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 = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   9920  Z= 0.287
  Angle     :  0.549   7.943  13425  Z= 0.289
  Chirality :  0.042   0.325   1430
  Planarity :  0.004   0.035   1705
  Dihedral  :  4.546  18.511   1300
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.69 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.24), residues: 1155
  helix:  1.09 (0.22), residues: 535
  sheet: -0.33 (0.27), residues: 310
  loop :  0.28 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Z 130 
 TYR   0.015   0.002   TYR Z  97 
 PHE   0.011   0.001   PHE Z 143 
 TRP   0.009   0.001   TRP Y 156 
 HIS   0.003   0.001   HIS W  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00611 ( 9920)
  covalent geometry    : angle       0.54896 (13425)
  hydrogen bonds       : bond        0.04040 (  569)
  hydrogen bonds       : angle       5.53521 ( 1572)

*********************** 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
  96 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.369 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.6995 (mp10) cc_final: 0.6515 (pp30)
REVERT: W    6 GLN cc_start: 0.6928 (mp10) cc_final: 0.6620 (pp30)
REVERT: X    6 GLN cc_start: 0.6952 (mp-120) cc_final: 0.6433 (tp40)
REVERT: X  161 MET cc_start: 0.8178 (tmm) cc_final: 0.7786 (tmt)
REVERT: Y    6 GLN cc_start: 0.6923 (mp10) cc_final: 0.6281 (tp40)
REVERT: Y  161 MET cc_start: 0.8230 (tmt) cc_final: 0.7971 (tmt)
REVERT: Z    6 GLN cc_start: 0.6967 (mp10) cc_final: 0.6603 (pp30)
REVERT: Z  161 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8021 (tmt)
REVERT: Z  239 MET cc_start: 0.9209 (mmp) cc_final: 0.8960 (mmp)
  outliers start: 27
  outliers final: 15
  residues processed: 93
  average time/residue: 0.6186
  time to fit residues: 61.4669
Evaluate side-chains
  82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
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   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  107 VAL
Chi-restraints excluded: chain X residue  110 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  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 93 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 114 optimal weight:    2.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
V 163 GLN
W 163 GLN
W 184 GLN
X 123 GLN
** Y 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.060619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.049817 restraints weight = 35907.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.70
r_work: 0.2962 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    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 = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9920  Z= 0.150
  Angle     :  0.495   8.819  13425  Z= 0.257
  Chirality :  0.041   0.367   1430
  Planarity :  0.003   0.035   1705
  Dihedral  :  4.391  17.322   1300
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.74 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.24), residues: 1155
  helix:  1.14 (0.22), residues: 540
  sheet: -0.38 (0.27), residues: 310
  loop :  0.21 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 130 
 TYR   0.013   0.001   TYR Z  97 
 PHE   0.010   0.001   PHE Z 195 
 TRP   0.013   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS Z  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9920)
  covalent geometry    : angle       0.49530 (13425)
  hydrogen bonds       : bond        0.03454 (  569)
  hydrogen bonds       : angle       5.37463 ( 1572)

*********************** 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: 21
    poor density    : 73
  time to evaluate  : 0.395 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7002 (mp10) cc_final: 0.6537 (pp30)
REVERT: W    6 GLN cc_start: 0.6924 (mp10) cc_final: 0.6608 (pp30)
REVERT: W   71 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9197 (tp)
REVERT: X    6 GLN cc_start: 0.6980 (mp-120) cc_final: 0.6436 (tp40)
REVERT: X  161 MET cc_start: 0.8173 (tmm) cc_final: 0.7745 (tmt)
REVERT: X  194 ASP cc_start: 0.8942 (m-30) cc_final: 0.8741 (m-30)
REVERT: Y    6 GLN cc_start: 0.6864 (mp10) cc_final: 0.6257 (tp40)
REVERT: Y  161 MET cc_start: 0.8197 (tmt) cc_final: 0.7943 (tmt)
REVERT: Z    6 GLN cc_start: 0.7065 (mp10) cc_final: 0.6721 (pp30)
REVERT: Z  161 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7975 (tmt)
REVERT: Z  239 MET cc_start: 0.9144 (mmp) cc_final: 0.8909 (mmp)
  outliers start: 21
  outliers final: 13
  residues processed: 89
  average time/residue: 0.5758
  time to fit residues: 55.1488
Evaluate side-chains
  86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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  110 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 89 optimal weight:    0.1980
   chunk 103 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 98 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.062095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.051265 restraints weight = 35445.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.75
r_work: 0.2983 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    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 = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9920  Z= 0.120
  Angle     :  0.466   8.620  13425  Z= 0.243
  Chirality :  0.040   0.345   1430
  Planarity :  0.003   0.035   1705
  Dihedral  :  4.220  17.577   1300
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.35 %
    Favored  : 99.57 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.84 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.24), residues: 1155
  helix:  1.28 (0.22), residues: 540
  sheet: -0.37 (0.27), residues: 310
  loop :  0.22 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG V 149 
 TYR   0.012   0.001   TYR Z  97 
 PHE   0.009   0.001   PHE Z 195 
 TRP   0.012   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS V  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9920)
  covalent geometry    : angle       0.46566 (13425)
  hydrogen bonds       : bond        0.03226 (  569)
  hydrogen bonds       : angle       5.24883 ( 1572)

*********************** 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
  94 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.383 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7134 (mp10) cc_final: 0.6639 (pp30)
REVERT: W    6 GLN cc_start: 0.6879 (mp10) cc_final: 0.6572 (pp30)
REVERT: W   71 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9195 (tp)
REVERT: X    6 GLN cc_start: 0.7016 (mp-120) cc_final: 0.6465 (tp40)
REVERT: X  161 MET cc_start: 0.8187 (tmm) cc_final: 0.7784 (tmt)
REVERT: X  194 ASP cc_start: 0.8831 (m-30) cc_final: 0.8621 (m-30)
REVERT: Y    6 GLN cc_start: 0.6938 (mp10) cc_final: 0.6350 (tp40)
REVERT: Y  161 MET cc_start: 0.8194 (tmt) cc_final: 0.7942 (tmt)
REVERT: Z    6 GLN cc_start: 0.7065 (mp10) cc_final: 0.6730 (pp30)
REVERT: Z  161 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7930 (tmt)
  outliers start: 19
  outliers final: 9
  residues processed: 88
  average time/residue: 0.6171
  time to fit residues: 58.0171
Evaluate side-chains
  82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
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 Y residue   99 LEU
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 27 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 109 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   chunk 100 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.062054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.051166 restraints weight = 35476.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.75
r_work: 0.2983 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2982
|-occupancy refinement: start-------------------------------------------------|
| 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 |
|-----------------------------------------------------------------------------|
|-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: 0.8781
moved from start:          0.3149

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= 0.127
  Angle     :  0.477   9.404  13425  Z= 0.245
  Chirality :  0.040   0.334   1430
  Planarity :  0.003   0.036   1705
  Dihedral  :  4.141  17.603   1300
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 19.71 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.24), residues: 1155
  helix:  1.29 (0.22), residues: 540
  sheet: -0.38 (0.27), residues: 310
  loop :  0.25 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG V 149 
 TYR   0.012   0.001   TYR Z  97 
 PHE   0.008   0.001   PHE X 143 
 TRP   0.013   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS V  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9920)
  covalent geometry    : angle       0.47687 (13425)
  hydrogen bonds       : bond        0.03196 (  569)
  hydrogen bonds       : angle       5.22653 ( 1572)

********************** 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
  91 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.380 
Fit side-chains
REVERT: V    6 GLN cc_start: 0.7116 (mp10) cc_final: 0.6631 (pp30)
REVERT: W    6 GLN cc_start: 0.6872 (mp10) cc_final: 0.6569 (pp30)
REVERT: W   71 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9182 (tp)
REVERT: X    6 GLN cc_start: 0.6988 (mp-120) cc_final: 0.6471 (tp40)
REVERT: X   71 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9268 (tp)
REVERT: X  161 MET cc_start: 0.8178 (tmm) cc_final: 0.7789 (tmt)
REVERT: X  194 ASP cc_start: 0.8849 (m-30) cc_final: 0.8589 (m-30)
REVERT: Y    6 GLN cc_start: 0.6944 (mp10) cc_final: 0.6354 (tp40)
REVERT: Y  161 MET cc_start: 0.8187 (tmt) cc_final: 0.7929 (tmt)
REVERT: Z    6 GLN cc_start: 0.6948 (mp10) cc_final: 0.6620 (pp30)
REVERT: Z  161 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7970 (tmt)
  outliers start: 15
  outliers final: 9
  residues processed: 88
  average time/residue: 0.6127
  time to fit residues: 57.8622
Evaluate side-chains
  83 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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 Y residue   99 LEU
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 29 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 184 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 = 0.3448 r_free = 0.3448 target = 0.061842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.050934 restraints weight = 35761.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.75
r_work: 0.2971 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    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 = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.3093

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= 0.148
  Angle     :  0.474   8.649  13425  Z= 0.246
  Chirality :  0.040   0.328   1430
  Planarity :  0.003   0.036   1705
  Dihedral  :  4.159  17.845   1300
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.26 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 19.52 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.24), residues: 1155
  helix:  1.28 (0.22), residues: 540
  sheet: -0.41 (0.27), residues: 310
  loop :  0.25 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG V 149 
 TYR   0.013   0.001   TYR Z  97 
 PHE   0.009   0.001   PHE X 143 
 TRP   0.011   0.001   TRP Y 156 
 HIS   0.002   0.001   HIS V  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9920)
  covalent geometry    : angle       0.47373 (13425)
  hydrogen bonds       : bond        0.03266 (  569)
  hydrogen bonds       : angle       5.26757 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3003.48 seconds
wall clock time: 52 minutes 4.63 seconds (3124.63 seconds total)