Starting phenix.real_space_refine
on Wed Apr 30 21:40:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhe_44542/04_2025/9bhe_44542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhe_44542/04_2025/9bhe_44542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bhe_44542/04_2025/9bhe_44542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhe_44542/04_2025/9bhe_44542.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhe_44542/04_2025/9bhe_44542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhe_44542/04_2025/9bhe_44542.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      52      5.16       5
     C    6302      2.51       5
     N    1702      2.21       5
     O    1814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9878
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2449
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 12, 'TRANS': 299}
    Chain: "B"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2440
          Classifications: {'peptide': 311}
          Link IDs: {'PTRANS': 12, 'TRANS': 298}
    Chain: "C"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2449
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 12, 'TRANS': 299}
    Chain: "D"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2440
          Classifications: {'peptide': 311}
          Link IDs: {'PTRANS': 12, 'TRANS': 298}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.55, per 1000 atoms: 0.66
  Number of scatterers: 9878
  At special positions: 0
  Unit cell: (109.254, 110.922, 98.412, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       8     15.00
     O    1814      8.00
     N    1702      7.00
     C    6302      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2324

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      57.5% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 38
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.714A  pdb=" N   LEU A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
      removed outlier: 3.831A  pdb=" N   HIS A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 109 through 118
      removed outlier: 3.532A  pdb=" N   LEU A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 153
    Processing helix  chain 'A' and resid 167 through 177
      removed outlier: 3.601A  pdb=" N   CYS A 177 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 191
    Processing helix  chain 'A' and resid 213 through 229
    Processing helix  chain 'A' and resid 230 through 261
      removed outlier: 4.130A  pdb=" N   ARG A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 303
      removed outlier: 3.919A  pdb=" N   PHE A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   THR A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 38
    Processing helix  chain 'B' and resid 53 through 64
      removed outlier: 3.709A  pdb=" N   LEU B  57 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 90
      removed outlier: 3.817A  pdb=" N   HIS B  90 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 108
      No H-bonds generated for 'chain 'B' and resid 106 through 108'
    Processing helix  chain 'B' and resid 109 through 118
      removed outlier: 3.521A  pdb=" N   LEU B 113 " --> pdb=" O   GLU B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 153
    Processing helix  chain 'B' and resid 167 through 177
    Processing helix  chain 'B' and resid 183 through 191
    Processing helix  chain 'B' and resid 213 through 229
      removed outlier: 3.586A  pdb=" N   THR B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 260
      removed outlier: 4.276A  pdb=" N   ARG B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 235 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B 236 " --> pdb=" O   PRO B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 303
      removed outlier: 3.604A  pdb=" N   LEU B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   VAL B 276 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 38
    Processing helix  chain 'C' and resid 53 through 64
      removed outlier: 3.715A  pdb=" N   LEU C  57 " --> pdb=" O   SER C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.832A  pdb=" N   HIS C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 108
      No H-bonds generated for 'chain 'C' and resid 106 through 108'
    Processing helix  chain 'C' and resid 109 through 118
      removed outlier: 3.532A  pdb=" N   LEU C 113 " --> pdb=" O   GLU C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 153
    Processing helix  chain 'C' and resid 167 through 177
      removed outlier: 3.596A  pdb=" N   CYS C 177 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 191
    Processing helix  chain 'C' and resid 213 through 229
    Processing helix  chain 'C' and resid 230 through 261
      removed outlier: 4.117A  pdb=" N   ARG C 234 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 304
    Processing helix  chain 'D' and resid 22 through 38
    Processing helix  chain 'D' and resid 53 through 64
      removed outlier: 3.712A  pdb=" N   LEU D  57 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 90
      removed outlier: 3.816A  pdb=" N   HIS D  90 " --> pdb=" O   ALA D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 108
      No H-bonds generated for 'chain 'D' and resid 106 through 108'
    Processing helix  chain 'D' and resid 109 through 118
      removed outlier: 3.521A  pdb=" N   LEU D 113 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 153
    Processing helix  chain 'D' and resid 167 through 177
    Processing helix  chain 'D' and resid 183 through 191
    Processing helix  chain 'D' and resid 213 through 229
      removed outlier: 3.587A  pdb=" N   THR D 229 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 260
      removed outlier: 4.257A  pdb=" N   ARG D 234 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU D 235 " --> pdb=" O   THR D 231 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU D 236 " --> pdb=" O   PRO D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 303
      removed outlier: 3.721A  pdb=" N   VAL D 276 " --> pdb=" O   MET D 272 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 200
      removed outlier: 3.633A  pdb=" N   ARG A 164 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   SER A  11 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ILE A  97 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL A  10 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   LEU A  44 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL A  12 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   ILE A  46 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE A  14 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 313
      removed outlier: 8.764A  pdb=" N   ILE D  70 " --> pdb=" O   TRP D  41 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE D  43 " --> pdb=" O   ILE D  70 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ILE D  72 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   LEU D  45 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   LEU D  74 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ASP D  47 " --> pdb=" O   LEU D  74 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL D  10 " --> pdb=" O   GLU D  42 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   LEU D  44 " --> pdb=" O   VAL D  10 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL D  12 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   ILE D  46 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE D  14 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER D  11 " --> pdb=" O   LEU D  95 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 198
      removed outlier: 4.011A  pdb=" N   SER B  11 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL B  10 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   LEU B  44 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL B  12 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ILE B  46 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE B  14 " --> pdb=" O   ILE B  46 " (cutoff:3.500A)
      removed outlier: 8.773A  pdb=" N   ILE B  70 " --> pdb=" O   TRP B  41 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ILE B  43 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ILE B  72 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   LEU B  45 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   LEU B  74 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ASP B  47 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 200
      removed outlier: 3.635A  pdb=" N   ARG C 164 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   SER C  11 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL C  10 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   LEU C  44 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL C  12 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   ILE C  46 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE C  14 " --> pdb=" O   ILE C  46 " (cutoff:3.500A)

    573 hydrogen bonds defined for protein.
    1707 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: 2.70

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 2181
        1.33 -     1.46: 2047
        1.46 -     1.59: 5750
        1.59 -     1.72: 0
        1.72 -     1.85: 88
  Bond restraints: 10066
  Sorted by residual:
  bond pdb=" C   LEU C 290 "
       pdb=" O   LEU C 290 "
    ideal  model  delta    sigma   weight residual
    1.236  1.296 -0.059 1.15e-02 7.56e+03 2.67e+01
  bond pdb=" C   LEU D 290 "
       pdb=" O   LEU D 290 "
    ideal  model  delta    sigma   weight residual
    1.236  1.291 -0.055 1.15e-02 7.56e+03 2.27e+01
  bond pdb=" C   VAL B 200 "
       pdb=" O   VAL B 200 "
    ideal  model  delta    sigma   weight residual
    1.235  1.275 -0.041 1.02e-02 9.61e+03 1.58e+01
  bond pdb=" CE1 HIS A 178 "
       pdb=" NE2 HIS A 178 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.44e+01
  bond pdb=" C   PRO D 199 "
       pdb=" O   PRO D 199 "
    ideal  model  delta    sigma   weight residual
    1.234  1.195  0.039 1.08e-02 8.57e+03 1.29e+01
  ... (remaining 10061 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 10156
        1.65 -     3.31: 3198
        3.31 -     4.96: 271
        4.96 -     6.61: 21
        6.61 -     8.27: 2
  Bond angle restraints: 13648
  Sorted by residual:
  angle pdb=" C   ARG A 128 "
        pdb=" CA  ARG A 128 "
        pdb=" CB  ARG A 128 "
      ideal   model   delta    sigma   weight residual
     110.77  118.70   -7.93 1.67e+00 3.59e-01 2.26e+01
  angle pdb=" C   PRO A 306 "
        pdb=" N   ARG A 307 "
        pdb=" CA  ARG A 307 "
      ideal   model   delta    sigma   weight residual
     120.28  126.31   -6.03 1.34e+00 5.57e-01 2.02e+01
  angle pdb=" CA  GLY D  79 "
        pdb=" C   GLY D  79 "
        pdb=" O   GLY D  79 "
      ideal   model   delta    sigma   weight residual
     121.77  117.97    3.80 8.60e-01 1.35e+00 1.95e+01
  angle pdb=" N   ILE B 298 "
        pdb=" CA  ILE B 298 "
        pdb=" C   ILE B 298 "
      ideal   model   delta    sigma   weight residual
     110.36  105.79    4.57 1.05e+00 9.07e-01 1.90e+01
  angle pdb=" N   TYR B 222 "
        pdb=" CA  TYR B 222 "
        pdb=" C   TYR B 222 "
      ideal   model   delta    sigma   weight residual
     111.14  106.48    4.66 1.08e+00 8.57e-01 1.86e+01
  ... (remaining 13643 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 5443
       16.75 -    33.50: 531
       33.50 -    50.25: 98
       50.25 -    67.00: 58
       67.00 -    83.75: 30
  Dihedral angle restraints: 6160
    sinusoidal: 2554
      harmonic: 3606
  Sorted by residual:
  dihedral pdb=" CA  TYR C 308 "
           pdb=" C   TYR C 308 "
           pdb=" N   PHE C 309 "
           pdb=" CA  PHE C 309 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.39   17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  MET D 156 "
           pdb=" C   MET D 156 "
           pdb=" N   GLY D 157 "
           pdb=" CA  GLY D 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  MET B 156 "
           pdb=" C   MET B 156 "
           pdb=" N   GLY B 157 "
           pdb=" CA  GLY B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.14  -16.86     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 674
       0.049 -    0.097: 511
       0.097 -    0.146: 288
       0.146 -    0.194: 105
       0.194 -    0.243: 8
  Chirality restraints: 1586
  Sorted by residual:
  chirality pdb=" CB  VAL D 302 "
            pdb=" CA  VAL D 302 "
            pdb=" CG1 VAL D 302 "
            pdb=" CG2 VAL D 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CB  VAL A 270 "
            pdb=" CA  VAL A 270 "
            pdb=" CG1 VAL A 270 "
            pdb=" CG2 VAL A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE B 298 "
            pdb=" N   ILE B 298 "
            pdb=" C   ILE B 298 "
            pdb=" CB  ILE B 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1583 not shown)

  Planarity restraints: 1720
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 222 "    0.076 2.00e-02 2.50e+03   4.32e-02 3.74e+01
        pdb=" CG  TYR D 222 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 222 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 222 "   -0.061 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 222 "    0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 222 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 222 "    0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR D 222 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 299 "   -0.060 2.00e-02 2.50e+03   3.44e-02 2.36e+01
        pdb=" CG  TYR A 299 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 299 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 299 "    0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 299 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 299 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 299 "   -0.023 2.00e-02 2.50e+03
        pdb=" OH  TYR A 299 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 299 "   -0.054 2.00e-02 2.50e+03   3.15e-02 1.99e+01
        pdb=" CG  TYR C 299 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 299 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 299 "    0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 299 "    0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 299 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 299 "   -0.019 2.00e-02 2.50e+03
        pdb=" OH  TYR C 299 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1717 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 566
        2.74 -     3.28: 11494
        3.28 -     3.82: 16386
        3.82 -     4.36: 20692
        4.36 -     4.90: 32179
  Nonbonded interactions: 81317
  Sorted by model distance:
  nonbonded pdb=" O   GLU B  64 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   VAL A 276 "
            pdb=" OG1 THR A 279 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   GLU D  64 "
            pdb=" OG  SER D  67 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OE1 GLU A  42 "
            pdb=" OG  SER A  92 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE1 GLU C  42 "
            pdb=" OG  SER C  92 "
     model   vdw
     2.217 3.040
  ... (remaining 81312 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 316 or resid 401))
  selection = chain 'B'
  selection = (chain 'C' and (resid 6 through 316 or resid 401))
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.620
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
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   0.086  10066  Z= 0.933
  Angle     :  1.434   8.267  13648  Z= 1.060
  Chirality :  0.081   0.243   1586
  Planarity :  0.009   0.128   1720
  Dihedral  : 15.876  83.751   3836
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.20 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.23), residues: 1238
  helix:  1.08 (0.20), residues: 678
  sheet: -0.65 (0.44), residues: 160
  loop : -1.57 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP A  41 
 HIS   0.019   0.006   HIS D  68 
 PHE   0.029   0.005   PHE A 280 
 TYR   0.076   0.012   TYR D 222 
 ARG   0.029   0.003   ARG D 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15389 (  573)
  hydrogen bonds       : angle       6.26979 ( 1707)
  covalent geometry    : bond        0.01255 (10066)
  covalent geometry    : angle       1.43386 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9760 (mmp) cc_final: 0.9343 (mmm)
REVERT: A  274 PHE cc_start: 0.9808 (m-80) cc_final: 0.9529 (m-80)
REVERT: B  156 MET cc_start: 0.7764 (tmm) cc_final: 0.7432 (tmm)
REVERT: B  212 TYR cc_start: 0.9166 (m-80) cc_final: 0.8614 (m-80)
REVERT: B  222 TYR cc_start: 0.9030 (t80) cc_final: 0.8652 (t80)
REVERT: B  272 MET cc_start: 0.9262 (mtm) cc_final: 0.8917 (mmm)
REVERT: C   58 MET cc_start: 0.9836 (mmp) cc_final: 0.9316 (mmm)
REVERT: C  301 ASP cc_start: 0.9557 (p0) cc_final: 0.9215 (m-30)
REVERT: D  212 TYR cc_start: 0.9172 (m-80) cc_final: 0.8747 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 73
  average time/residue: 0.2065
  time to fit residues: 22.7136
Evaluate side-chains
  51 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.036897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.029878 restraints weight = 87513.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.030820 restraints weight = 50878.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.031412 restraints weight = 34120.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10066  Z= 0.170
  Angle     :  0.654   7.343  13648  Z= 0.344
  Chirality :  0.043   0.146   1586
  Planarity :  0.004   0.051   1720
  Dihedral  : 12.690  72.273   1502
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  5.46 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.24), residues: 1238
  helix:  1.90 (0.20), residues: 698
  sheet: -1.00 (0.42), residues: 168
  loop : -1.74 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  41 
 HIS   0.011   0.001   HIS A 178 
 PHE   0.018   0.001   PHE C 274 
 TYR   0.018   0.002   TYR A 159 
 ARG   0.004   0.001   ARG C 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04307 (  573)
  hydrogen bonds       : angle       4.86279 ( 1707)
  covalent geometry    : bond        0.00370 (10066)
  covalent geometry    : angle       0.65439 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9563 (mmp) cc_final: 0.9293 (mmm)
REVERT: A  274 PHE cc_start: 0.9797 (m-80) cc_final: 0.9357 (m-10)
REVERT: B   85 MET cc_start: 0.9420 (tpt) cc_final: 0.9200 (mmm)
REVERT: B  156 MET cc_start: 0.7781 (tmm) cc_final: 0.7543 (tmm)
REVERT: B  221 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8580 (ppp)
REVERT: C   58 MET cc_start: 0.9577 (mmp) cc_final: 0.9292 (mmm)
REVERT: D  156 MET cc_start: 0.8206 (tmm) cc_final: 0.7948 (tmm)
REVERT: D  221 MET cc_start: 0.9167 (pmm) cc_final: 0.8962 (pmm)
  outliers start: 13
  outliers final: 4
  residues processed: 69
  average time/residue: 0.1953
  time to fit residues: 21.0848
Evaluate side-chains
  54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue  242 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 118 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 123 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.035509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.028576 restraints weight = 92680.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.029512 restraints weight = 54517.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.030028 restraints weight = 37048.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  10066  Z= 0.235
  Angle     :  0.668   6.988  13648  Z= 0.360
  Chirality :  0.041   0.141   1586
  Planarity :  0.004   0.051   1720
  Dihedral  : 11.681  78.750   1502
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.51 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.24), residues: 1238
  helix:  2.00 (0.20), residues: 698
  sheet: -0.84 (0.42), residues: 164
  loop : -1.60 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  41 
 HIS   0.017   0.002   HIS C 178 
 PHE   0.010   0.001   PHE B 214 
 TYR   0.020   0.002   TYR A 308 
 ARG   0.003   0.001   ARG D 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  573)
  hydrogen bonds       : angle       4.70497 ( 1707)
  covalent geometry    : bond        0.00499 (10066)
  covalent geometry    : angle       0.66755 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9616 (mmp) cc_final: 0.9283 (mmm)
REVERT: A  274 PHE cc_start: 0.9818 (m-80) cc_final: 0.9409 (m-80)
REVERT: B   85 MET cc_start: 0.9499 (tpt) cc_final: 0.9269 (mmm)
REVERT: B  156 MET cc_start: 0.7966 (tmm) cc_final: 0.7643 (tmm)
REVERT: B  221 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8709 (ppp)
REVERT: B  272 MET cc_start: 0.8845 (ptt) cc_final: 0.7935 (mmt)
REVERT: C   58 MET cc_start: 0.9595 (mmp) cc_final: 0.9255 (mmm)
REVERT: D  156 MET cc_start: 0.8422 (tmm) cc_final: 0.8132 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 58
  average time/residue: 0.1928
  time to fit residues: 17.2700
Evaluate side-chains
  56 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue  221 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 108 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 GLN
D  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.034970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.028039 restraints weight = 92839.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.028920 restraints weight = 56112.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.029452 restraints weight = 39066.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  10066  Z= 0.263
  Angle     :  0.674   7.033  13648  Z= 0.357
  Chirality :  0.041   0.140   1586
  Planarity :  0.004   0.052   1720
  Dihedral  :  9.251  86.160   1502
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.11 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.24), residues: 1238
  helix:  1.95 (0.19), residues: 700
  sheet: -0.81 (0.42), residues: 164
  loop : -1.49 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  41 
 HIS   0.015   0.001   HIS A 178 
 PHE   0.013   0.001   PHE B 285 
 TYR   0.020   0.002   TYR A 308 
 ARG   0.003   0.001   ARG B 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03966 (  573)
  hydrogen bonds       : angle       4.68416 ( 1707)
  covalent geometry    : bond        0.00547 (10066)
  covalent geometry    : angle       0.67400 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9608 (mmp) cc_final: 0.9276 (mmm)
REVERT: A  274 PHE cc_start: 0.9827 (m-80) cc_final: 0.9400 (m-80)
REVERT: A  308 TYR cc_start: 0.8900 (p90) cc_final: 0.8574 (p90)
REVERT: B   85 MET cc_start: 0.9531 (tpt) cc_final: 0.9324 (mmm)
REVERT: B  156 MET cc_start: 0.8166 (tmm) cc_final: 0.7951 (tmm)
REVERT: B  272 MET cc_start: 0.8877 (ptt) cc_final: 0.8038 (mmt)
REVERT: B  301 ASP cc_start: 0.9459 (m-30) cc_final: 0.9000 (m-30)
REVERT: C   58 MET cc_start: 0.9617 (mmp) cc_final: 0.9258 (mmm)
REVERT: C  308 TYR cc_start: 0.8910 (p90) cc_final: 0.8608 (p90)
REVERT: D  156 MET cc_start: 0.8560 (tmm) cc_final: 0.8239 (tmm)
REVERT: D  301 ASP cc_start: 0.9443 (m-30) cc_final: 0.8925 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 61
  average time/residue: 0.1900
  time to fit residues: 18.0409
Evaluate side-chains
  61 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 35 optimal weight:    0.0970
   chunk 51 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0070
   chunk 12 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   chunk 123 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 284 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 = 0.3041 r_free = 0.3041 target = 0.036330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.029340 restraints weight = 87342.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.030257 restraints weight = 52595.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.030801 restraints weight = 36151.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10066  Z= 0.110
  Angle     :  0.593   7.637  13648  Z= 0.299
  Chirality :  0.042   0.142   1586
  Planarity :  0.004   0.052   1720
  Dihedral  :  8.773  83.780   1502
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.83 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.24), residues: 1238
  helix:  2.13 (0.20), residues: 698
  sheet: -0.64 (0.42), residues: 164
  loop : -1.63 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  41 
 HIS   0.010   0.001   HIS A 178 
 PHE   0.007   0.001   PHE D 280 
 TYR   0.012   0.001   TYR A 159 
 ARG   0.004   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03400 (  573)
  hydrogen bonds       : angle       4.14352 ( 1707)
  covalent geometry    : bond        0.00225 (10066)
  covalent geometry    : angle       0.59284 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9066 (mm)
REVERT: A   58 MET cc_start: 0.9587 (mmp) cc_final: 0.9160 (mmm)
REVERT: A  221 MET cc_start: 0.9356 (ppp) cc_final: 0.9047 (ppp)
REVERT: A  274 PHE cc_start: 0.9802 (m-80) cc_final: 0.9337 (m-80)
REVERT: B   85 MET cc_start: 0.9546 (tpt) cc_final: 0.9341 (mmm)
REVERT: B  272 MET cc_start: 0.8914 (ptt) cc_final: 0.8023 (mmt)
REVERT: B  301 ASP cc_start: 0.9491 (m-30) cc_final: 0.8904 (m-30)
REVERT: C   45 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9070 (mm)
REVERT: C   58 MET cc_start: 0.9587 (mmp) cc_final: 0.9120 (mmm)
REVERT: D  156 MET cc_start: 0.8543 (tmm) cc_final: 0.8274 (tmm)
REVERT: D  272 MET cc_start: 0.9422 (mmt) cc_final: 0.8781 (mmm)
REVERT: D  301 ASP cc_start: 0.9405 (m-30) cc_final: 0.8884 (m-30)
  outliers start: 19
  outliers final: 7
  residues processed: 69
  average time/residue: 0.1844
  time to fit residues: 19.9500
Evaluate side-chains
  62 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   63 GLN
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 117 optimal weight:    0.9990
   chunk 110 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0970
   chunk 3 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 85 optimal weight:    9.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.035743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.028730 restraints weight = 91436.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.029614 restraints weight = 55005.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.030209 restraints weight = 38263.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10066  Z= 0.167
  Angle     :  0.628   8.671  13648  Z= 0.318
  Chirality :  0.041   0.173   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.817  86.292   1502
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.43 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.24), residues: 1238
  helix:  2.16 (0.19), residues: 698
  sheet: -0.50 (0.44), residues: 164
  loop : -1.56 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  41 
 HIS   0.003   0.001   HIS D 201 
 PHE   0.007   0.001   PHE B 285 
 TYR   0.013   0.001   TYR C 308 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03406 (  573)
  hydrogen bonds       : angle       4.26578 ( 1707)
  covalent geometry    : bond        0.00355 (10066)
  covalent geometry    : angle       0.62764 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9572 (mmp) cc_final: 0.9207 (mmm)
REVERT: A  221 MET cc_start: 0.9384 (ppp) cc_final: 0.9084 (ppp)
REVERT: A  274 PHE cc_start: 0.9821 (m-80) cc_final: 0.9374 (m-80)
REVERT: A  308 TYR cc_start: 0.8915 (p90) cc_final: 0.8507 (p90)
REVERT: B   85 MET cc_start: 0.9571 (tpt) cc_final: 0.9359 (mmm)
REVERT: B  222 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8062 (t80)
REVERT: B  272 MET cc_start: 0.8953 (ptt) cc_final: 0.8073 (mmt)
REVERT: B  301 ASP cc_start: 0.9473 (m-30) cc_final: 0.8921 (m-30)
REVERT: C   58 MET cc_start: 0.9597 (mmp) cc_final: 0.9217 (mmm)
REVERT: D  272 MET cc_start: 0.9429 (mmt) cc_final: 0.8777 (mmm)
REVERT: D  301 ASP cc_start: 0.9411 (m-30) cc_final: 0.8915 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 68
  average time/residue: 0.2236
  time to fit residues: 23.9508
Evaluate side-chains
  64 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   63 GLN
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 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 = 0.3004 r_free = 0.3004 target = 0.035133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.028213 restraints weight = 91798.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.029103 restraints weight = 55409.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.029606 restraints weight = 38349.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10066  Z= 0.205
  Angle     :  0.663   8.391  13648  Z= 0.338
  Chirality :  0.041   0.157   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.980  89.112   1502
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.62 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.24), residues: 1238
  helix:  2.08 (0.19), residues: 700
  sheet: -0.49 (0.43), residues: 164
  loop : -1.51 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  41 
 HIS   0.005   0.001   HIS B  81 
 PHE   0.008   0.001   PHE B 285 
 TYR   0.013   0.001   TYR C 308 
 ARG   0.003   0.000   ARG D 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  573)
  hydrogen bonds       : angle       4.32231 ( 1707)
  covalent geometry    : bond        0.00435 (10066)
  covalent geometry    : angle       0.66276 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9583 (mmp) cc_final: 0.9230 (mmm)
REVERT: A  221 MET cc_start: 0.9384 (ppp) cc_final: 0.9100 (ppp)
REVERT: A  274 PHE cc_start: 0.9819 (m-80) cc_final: 0.9364 (m-80)
REVERT: A  308 TYR cc_start: 0.8989 (p90) cc_final: 0.8578 (p90)
REVERT: B   85 MET cc_start: 0.9537 (tpt) cc_final: 0.9310 (mmm)
REVERT: B  222 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8121 (t80)
REVERT: B  272 MET cc_start: 0.9014 (ptt) cc_final: 0.8173 (mmt)
REVERT: B  301 ASP cc_start: 0.9425 (m-30) cc_final: 0.8840 (m-30)
REVERT: C   58 MET cc_start: 0.9594 (mmp) cc_final: 0.9228 (mmm)
REVERT: D  222 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8200 (t80)
REVERT: D  301 ASP cc_start: 0.9376 (m-30) cc_final: 0.8869 (m-30)
  outliers start: 19
  outliers final: 13
  residues processed: 71
  average time/residue: 0.2165
  time to fit residues: 23.8536
Evaluate side-chains
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   63 GLN
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 118 optimal weight:   20.0000
   chunk 82 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0030
   overall best weight:    1.0794

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 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 = 0.3028 r_free = 0.3028 target = 0.035932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.028952 restraints weight = 90145.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.029851 restraints weight = 54528.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.030454 restraints weight = 37906.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10066  Z= 0.118
  Angle     :  0.648  10.354  13648  Z= 0.321
  Chirality :  0.042   0.149   1586
  Planarity :  0.004   0.050   1720
  Dihedral  :  9.000  89.781   1502
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.34 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1238
  helix:  2.15 (0.19), residues: 700
  sheet: -0.40 (0.44), residues: 164
  loop : -1.55 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  41 
 HIS   0.003   0.001   HIS D  81 
 PHE   0.004   0.001   PHE D 280 
 TYR   0.010   0.001   TYR C 308 
 ARG   0.004   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03350 (  573)
  hydrogen bonds       : angle       4.10403 ( 1707)
  covalent geometry    : bond        0.00259 (10066)
  covalent geometry    : angle       0.64803 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9005 (mp)
REVERT: A   58 MET cc_start: 0.9565 (mmp) cc_final: 0.9163 (mmm)
REVERT: A  221 MET cc_start: 0.9385 (ppp) cc_final: 0.9091 (ppp)
REVERT: A  274 PHE cc_start: 0.9805 (m-80) cc_final: 0.9333 (m-80)
REVERT: A  308 TYR cc_start: 0.8961 (p90) cc_final: 0.8687 (p90)
REVERT: B   85 MET cc_start: 0.9538 (tpt) cc_final: 0.9302 (mmm)
REVERT: B  221 MET cc_start: 0.9171 (ptp) cc_final: 0.8890 (ptp)
REVERT: B  222 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8046 (t80)
REVERT: B  272 MET cc_start: 0.8984 (ptt) cc_final: 0.8140 (mmt)
REVERT: B  301 ASP cc_start: 0.9441 (m-30) cc_final: 0.8846 (m-30)
REVERT: C   45 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9015 (mp)
REVERT: C   58 MET cc_start: 0.9583 (mmp) cc_final: 0.9150 (mmm)
REVERT: D  272 MET cc_start: 0.9448 (mmt) cc_final: 0.8849 (mmm)
REVERT: D  301 ASP cc_start: 0.9392 (m-30) cc_final: 0.8876 (m-30)
  outliers start: 22
  outliers final: 11
  residues processed: 78
  average time/residue: 0.2406
  time to fit residues: 29.5696
Evaluate side-chains
  70 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 120 optimal weight:    0.8980
   chunk 46 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 119 optimal weight:    6.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 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 = 0.3037 r_free = 0.3037 target = 0.036121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.029105 restraints weight = 88097.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.029994 restraints weight = 53455.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.030624 restraints weight = 37188.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10066  Z= 0.114
  Angle     :  0.657  10.145  13648  Z= 0.320
  Chirality :  0.043   0.290   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.946  89.818   1502
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.90 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.24), residues: 1238
  helix:  2.07 (0.19), residues: 698
  sheet: -0.48 (0.43), residues: 168
  loop : -1.54 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  41 
 HIS   0.002   0.001   HIS B  68 
 PHE   0.007   0.001   PHE C 274 
 TYR   0.008   0.001   TYR C 308 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03245 (  573)
  hydrogen bonds       : angle       4.02564 ( 1707)
  covalent geometry    : bond        0.00247 (10066)
  covalent geometry    : angle       0.65711 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8950 (mm)
REVERT: A   58 MET cc_start: 0.9599 (mmp) cc_final: 0.9174 (mmm)
REVERT: A  221 MET cc_start: 0.9374 (ppp) cc_final: 0.9077 (ppp)
REVERT: A  274 PHE cc_start: 0.9787 (m-80) cc_final: 0.9325 (m-80)
REVERT: A  308 TYR cc_start: 0.8933 (p90) cc_final: 0.8629 (p90)
REVERT: B   85 MET cc_start: 0.9546 (tpt) cc_final: 0.9290 (mmm)
REVERT: B  222 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8026 (t80)
REVERT: B  272 MET cc_start: 0.8980 (ptt) cc_final: 0.8143 (mmt)
REVERT: B  301 ASP cc_start: 0.9398 (m-30) cc_final: 0.8818 (m-30)
REVERT: C   45 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9021 (mm)
REVERT: C   58 MET cc_start: 0.9575 (mmp) cc_final: 0.9137 (mmm)
REVERT: D  162 MET cc_start: 0.9100 (mtp) cc_final: 0.8613 (mtt)
REVERT: D  221 MET cc_start: 0.9307 (ptp) cc_final: 0.8940 (ppp)
REVERT: D  222 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8036 (t80)
REVERT: D  272 MET cc_start: 0.9403 (mmt) cc_final: 0.8738 (mmm)
REVERT: D  301 ASP cc_start: 0.9379 (m-30) cc_final: 0.8849 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 72
  average time/residue: 0.2046
  time to fit residues: 23.3361
Evaluate side-chains
  72 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 85 optimal weight:    7.9990
   chunk 114 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 109 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 119 optimal weight:    0.9990
   chunk 104 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 284 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 = 0.3036 r_free = 0.3036 target = 0.036106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.029047 restraints weight = 87634.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.029951 restraints weight = 53473.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.030562 restraints weight = 37349.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10066  Z= 0.119
  Angle     :  0.654  10.372  13648  Z= 0.320
  Chirality :  0.042   0.268   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.879  89.608   1502
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.37 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.24), residues: 1238
  helix:  2.08 (0.19), residues: 696
  sheet: -0.45 (0.43), residues: 168
  loop : -1.55 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  41 
 HIS   0.002   0.001   HIS B  68 
 PHE   0.038   0.001   PHE C 274 
 TYR   0.009   0.001   TYR C 308 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03193 (  573)
  hydrogen bonds       : angle       4.02752 ( 1707)
  covalent geometry    : bond        0.00261 (10066)
  covalent geometry    : angle       0.65408 (13648)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8928 (mm)
REVERT: A   58 MET cc_start: 0.9605 (mmp) cc_final: 0.9191 (mmm)
REVERT: A  221 MET cc_start: 0.9376 (ppp) cc_final: 0.9076 (ppp)
REVERT: A  274 PHE cc_start: 0.9785 (m-80) cc_final: 0.9346 (m-80)
REVERT: A  308 TYR cc_start: 0.8923 (p90) cc_final: 0.8615 (p90)
REVERT: B   85 MET cc_start: 0.9556 (tpt) cc_final: 0.9296 (mmm)
REVERT: B  221 MET cc_start: 0.9170 (ptp) cc_final: 0.8877 (ptp)
REVERT: B  222 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8030 (t80)
REVERT: B  272 MET cc_start: 0.8980 (ptt) cc_final: 0.8133 (mmt)
REVERT: B  301 ASP cc_start: 0.9384 (m-30) cc_final: 0.8814 (m-30)
REVERT: C   45 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8967 (mm)
REVERT: C   58 MET cc_start: 0.9588 (mmp) cc_final: 0.9167 (mmm)
REVERT: C  288 MET cc_start: 0.9250 (mmm) cc_final: 0.8848 (mmm)
REVERT: D  162 MET cc_start: 0.9104 (mtp) cc_final: 0.8617 (mtt)
REVERT: D  222 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8073 (t80)
REVERT: D  272 MET cc_start: 0.9378 (mmt) cc_final: 0.8676 (mmm)
REVERT: D  301 ASP cc_start: 0.9369 (m-30) cc_final: 0.8850 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1866
  time to fit residues: 20.1666
Evaluate side-chains
  70 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 89 optimal weight:    0.8980
   chunk 87 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 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 = 0.3020 r_free = 0.3020 target = 0.035803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.028642 restraints weight = 91483.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.029508 restraints weight = 56407.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.030056 restraints weight = 39883.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10066  Z= 0.157
  Angle     :  0.672   9.993  13648  Z= 0.334
  Chirality :  0.042   0.197   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.899  89.439   1502
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.56 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.25), residues: 1238
  helix:  2.09 (0.20), residues: 702
  sheet: -0.36 (0.44), residues: 168
  loop : -1.51 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  41 
 HIS   0.003   0.001   HIS D  81 
 PHE   0.015   0.001   PHE C 274 
 TYR   0.010   0.001   TYR C 308 
 ARG   0.002   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (  573)
  hydrogen bonds       : angle       4.13268 ( 1707)
  covalent geometry    : bond        0.00342 (10066)
  covalent geometry    : angle       0.67203 (13648)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3009.89 seconds
wall clock time: 54 minutes 31.44 seconds (3271.44 seconds total)