Starting phenix.real_space_refine
on Wed Jul 30 04:36:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lic_23372/07_2025/7lic_23372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lic_23372/07_2025/7lic_23372.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lic_23372/07_2025/7lic_23372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lic_23372/07_2025/7lic_23372.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lic_23372/07_2025/7lic_23372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lic_23372/07_2025/7lic_23372.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     120      5.16       5
     C    7888      2.51       5
     N    1920      2.21       5
     O    2052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11980
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2995
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 9, 'TRANS': 367}
          Chain breaks: 3
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 6.16, per 1000 atoms: 0.51
  Number of scatterers: 11980
  At special positions: 0
  Unit cell: (111.24, 110.21, 89.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     120     16.00
     O    2052      8.00
     N    1920      7.00
     C    7888      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: 2.79
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2896

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      83.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 31
      removed outlier: 3.633A  pdb=" N   HIS A  16 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 47
      removed outlier: 3.760A  pdb=" N   LYS A  47 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 44 through 47'
    Processing helix  chain 'A' and resid 48 through 75
    Processing helix  chain 'A' and resid 78 through 105
      removed outlier: 3.646A  pdb=" N   LEU A  83 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   VAL A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 118
      removed outlier: 3.851A  pdb=" N   GLU A 118 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 167
      removed outlier: 3.816A  pdb=" N   SER A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LEU A 161 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
      removed outlier: 3.606A  pdb=" N   LEU A 166 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 247
      removed outlier: 3.767A  pdb=" N   GLU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA A 215 " --> pdb=" O   PHE A 211 " (cutoff:3.500A)
      Proline residue:  A 216  - end of helix
    Processing helix  chain 'A' and resid 318 through 366
      removed outlier: 3.841A  pdb=" N   SER A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   SER A 344 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   TYR A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ALA A 366 " --> pdb=" O   TYR A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 407
      removed outlier: 4.265A  pdb=" N   GLY A 376 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 387 " --> pdb=" O   TYR A 383 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ALA A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 416
    Processing helix  chain 'A' and resid 418 through 433
      removed outlier: 3.682A  pdb=" N   GLN A 426 " --> pdb=" O   ARG A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 468
    Processing helix  chain 'B' and resid 13 through 31
    Processing helix  chain 'B' and resid 44 through 47
      removed outlier: 3.760A  pdb=" N   LYS B  47 " --> pdb=" O   ASN B  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 44 through 47'
    Processing helix  chain 'B' and resid 48 through 75
    Processing helix  chain 'B' and resid 78 through 105
      removed outlier: 3.645A  pdb=" N   LEU B  83 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN B  84 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   THR B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   VAL B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 118
      removed outlier: 3.852A  pdb=" N   GLU B 118 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 167
      removed outlier: 3.816A  pdb=" N   SER B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LEU B 161 " --> pdb=" O   MET B 157 " (cutoff:3.500A)
      Proline residue:  B 162  - end of helix
      removed outlier: 3.605A  pdb=" N   LEU B 166 " --> pdb=" O   PRO B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 247
      removed outlier: 3.765A  pdb=" N   GLU B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA B 215 " --> pdb=" O   PHE B 211 " (cutoff:3.500A)
      Proline residue:  B 216  - end of helix
    Processing helix  chain 'B' and resid 318 through 366
      removed outlier: 3.841A  pdb=" N   SER B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER B 344 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   TYR B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ALA B 366 " --> pdb=" O   TYR B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 407
      removed outlier: 4.265A  pdb=" N   GLY B 376 " --> pdb=" O   THR B 372 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG B 387 " --> pdb=" O   TYR B 383 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   VAL B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ALA B 399 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 416
    Processing helix  chain 'B' and resid 418 through 433
      removed outlier: 3.683A  pdb=" N   GLN B 426 " --> pdb=" O   ARG B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 468
    Processing helix  chain 'C' and resid 13 through 31
    Processing helix  chain 'C' and resid 44 through 47
      removed outlier: 3.761A  pdb=" N   LYS C  47 " --> pdb=" O   ASN C  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 44 through 47'
    Processing helix  chain 'C' and resid 48 through 75
    Processing helix  chain 'C' and resid 78 through 105
      removed outlier: 3.645A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ASN C  84 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR C  87 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   VAL C  88 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 118
      removed outlier: 3.851A  pdb=" N   GLU C 118 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 167
      removed outlier: 3.815A  pdb=" N   SER C 131 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LEU C 161 " --> pdb=" O   MET C 157 " (cutoff:3.500A)
      Proline residue:  C 162  - end of helix
      removed outlier: 3.606A  pdb=" N   LEU C 166 " --> pdb=" O   PRO C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 247
      removed outlier: 3.767A  pdb=" N   GLU C 199 " --> pdb=" O   SER C 195 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ALA C 215 " --> pdb=" O   PHE C 211 " (cutoff:3.500A)
      Proline residue:  C 216  - end of helix
    Processing helix  chain 'C' and resid 318 through 366
      removed outlier: 3.841A  pdb=" N   SER C 343 " --> pdb=" O   GLN C 339 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   SER C 344 " --> pdb=" O   SER C 340 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   TYR C 345 " --> pdb=" O   VAL C 341 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ALA C 366 " --> pdb=" O   TYR C 362 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 407
      removed outlier: 4.265A  pdb=" N   GLY C 376 " --> pdb=" O   THR C 372 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG C 387 " --> pdb=" O   TYR C 383 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   VAL C 398 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ALA C 399 " --> pdb=" O   ALA C 395 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS C 407 " --> pdb=" O   LEU C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 412 through 416
    Processing helix  chain 'C' and resid 418 through 433
      removed outlier: 3.683A  pdb=" N   GLN C 426 " --> pdb=" O   ARG C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 447 through 468
    Processing helix  chain 'D' and resid 13 through 31
    Processing helix  chain 'D' and resid 44 through 47
      removed outlier: 3.761A  pdb=" N   LYS D  47 " --> pdb=" O   ASN D  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 44 through 47'
    Processing helix  chain 'D' and resid 48 through 75
    Processing helix  chain 'D' and resid 78 through 105
      removed outlier: 3.646A  pdb=" N   LEU D  83 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ASN D  84 " --> pdb=" O   ALA D  80 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR D  87 " --> pdb=" O   LEU D  83 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   VAL D  88 " --> pdb=" O   ASN D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 118
      removed outlier: 3.851A  pdb=" N   GLU D 118 " --> pdb=" O   ASN D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 167
      removed outlier: 3.816A  pdb=" N   SER D 131 " --> pdb=" O   GLY D 127 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LEU D 161 " --> pdb=" O   MET D 157 " (cutoff:3.500A)
      Proline residue:  D 162  - end of helix
      removed outlier: 3.605A  pdb=" N   LEU D 166 " --> pdb=" O   PRO D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 247
      removed outlier: 3.767A  pdb=" N   GLU D 199 " --> pdb=" O   SER D 195 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA D 215 " --> pdb=" O   PHE D 211 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 318 through 366
      removed outlier: 3.840A  pdb=" N   SER D 343 " --> pdb=" O   GLN D 339 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   SER D 344 " --> pdb=" O   SER D 340 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   TYR D 345 " --> pdb=" O   VAL D 341 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ALA D 366 " --> pdb=" O   TYR D 362 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 407
      removed outlier: 4.264A  pdb=" N   GLY D 376 " --> pdb=" O   THR D 372 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG D 387 " --> pdb=" O   TYR D 383 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   VAL D 398 " --> pdb=" O   LEU D 394 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ALA D 399 " --> pdb=" O   ALA D 395 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS D 407 " --> pdb=" O   LEU D 403 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 412 through 416
    Processing helix  chain 'D' and resid 418 through 433
      removed outlier: 3.683A  pdb=" N   GLN D 426 " --> pdb=" O   ARG D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 447 through 468

    972 hydrogen bonds defined for protein.
    2892 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.46

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3558
        1.34 -     1.46: 2825
        1.46 -     1.58: 5697
        1.58 -     1.69: 0
        1.69 -     1.81: 172
  Bond restraints: 12252
  Sorted by residual:
  bond pdb=" C   SER D 195 "
       pdb=" N   PRO D 196 "
    ideal  model  delta    sigma   weight residual
    1.336  1.368 -0.032 1.20e-02 6.94e+03 7.07e+00
  bond pdb=" C   SER C 195 "
       pdb=" N   PRO C 196 "
    ideal  model  delta    sigma   weight residual
    1.336  1.368 -0.032 1.20e-02 6.94e+03 6.96e+00
  bond pdb=" C   SER A 195 "
       pdb=" N   PRO A 196 "
    ideal  model  delta    sigma   weight residual
    1.336  1.367 -0.031 1.20e-02 6.94e+03 6.80e+00
  bond pdb=" C   SER B 195 "
       pdb=" N   PRO B 196 "
    ideal  model  delta    sigma   weight residual
    1.336  1.367 -0.031 1.20e-02 6.94e+03 6.67e+00
  bond pdb=" C   VAL D 374 "
       pdb=" N   PRO D 375 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 1.51e-02 4.39e+03 2.13e+00
  ... (remaining 12247 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 15678
        1.58 -     3.16: 758
        3.16 -     4.73: 144
        4.73 -     6.31: 24
        6.31 -     7.89: 8
  Bond angle restraints: 16612
  Sorted by residual:
  angle pdb=" CA  THR C 367 "
        pdb=" C   THR C 367 "
        pdb=" N   SER C 368 "
      ideal   model   delta    sigma   weight residual
     115.55  120.52   -4.97 1.33e+00 5.65e-01 1.40e+01
  angle pdb=" CA  THR A 367 "
        pdb=" C   THR A 367 "
        pdb=" N   SER A 368 "
      ideal   model   delta    sigma   weight residual
     115.55  120.51   -4.96 1.33e+00 5.65e-01 1.39e+01
  angle pdb=" C   THR A 367 "
        pdb=" CA  THR A 367 "
        pdb=" CB  THR A 367 "
      ideal   model   delta    sigma   weight residual
     109.50  115.79   -6.29 1.69e+00 3.50e-01 1.39e+01
  angle pdb=" CA  THR B 367 "
        pdb=" C   THR B 367 "
        pdb=" N   SER B 368 "
      ideal   model   delta    sigma   weight residual
     115.55  120.50   -4.95 1.33e+00 5.65e-01 1.39e+01
  angle pdb=" C   THR C 367 "
        pdb=" CA  THR C 367 "
        pdb=" CB  THR C 367 "
      ideal   model   delta    sigma   weight residual
     109.50  115.75   -6.25 1.69e+00 3.50e-01 1.37e+01
  ... (remaining 16607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 6414
       17.55 -    35.10: 598
       35.10 -    52.65: 152
       52.65 -    70.20: 24
       70.20 -    87.75: 8
  Dihedral angle restraints: 7196
    sinusoidal: 2740
      harmonic: 4456
  Sorted by residual:
  dihedral pdb=" CA  ASN A  85 "
           pdb=" C   ASN A  85 "
           pdb=" N   ILE A  86 "
           pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  ASN C  85 "
           pdb=" C   ASN C  85 "
           pdb=" N   ILE C  86 "
           pdb=" CA  ILE C  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.18  -20.82     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  ASN D  85 "
           pdb=" C   ASN D  85 "
           pdb=" N   ILE D  86 "
           pdb=" CA  ILE D  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.21  -20.79     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 7193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1275
       0.037 -    0.074: 522
       0.074 -    0.111: 151
       0.111 -    0.148: 32
       0.148 -    0.185: 12
  Chirality restraints: 1992
  Sorted by residual:
  chirality pdb=" CG  LEU D  83 "
            pdb=" CB  LEU D  83 "
            pdb=" CD1 LEU D  83 "
            pdb=" CD2 LEU D  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.57e-01
  chirality pdb=" CG  LEU B  83 "
            pdb=" CB  LEU B  83 "
            pdb=" CD1 LEU B  83 "
            pdb=" CD2 LEU B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.49e-01
  chirality pdb=" CG  LEU A  83 "
            pdb=" CB  LEU A  83 "
            pdb=" CD1 LEU A  83 "
            pdb=" CD2 LEU A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.44e-01
  ... (remaining 1989 not shown)

  Planarity restraints: 1988
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B  96 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.92e+00
        pdb=" C   CYS B  96 "    0.046 2.00e-02 2.50e+03
        pdb=" O   CYS B  96 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL B  97 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A  96 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.79e+00
        pdb=" C   CYS A  96 "    0.045 2.00e-02 2.50e+03
        pdb=" O   CYS A  96 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL A  97 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS C  96 "    0.013 2.00e-02 2.50e+03   2.60e-02 6.77e+00
        pdb=" C   CYS C  96 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   CYS C  96 "    0.017 2.00e-02 2.50e+03
        pdb=" N   VAL C  97 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1985 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3052
        2.79 -     3.32: 12148
        3.32 -     3.84: 19802
        3.84 -     4.37: 21248
        4.37 -     4.90: 37126
  Nonbonded interactions: 93376
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 397 "
            pdb=" NH1 ARG D 442 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OG  SER A  78 "
            pdb=" OE1 GLN A  81 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER D  78 "
            pdb=" OE1 GLN D  81 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER B  78 "
            pdb=" OE1 GLN B  81 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER C  78 "
            pdb=" OE1 GLN C  81 "
     model   vdw
     2.282 3.040
  ... (remaining 93371 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: 0.13
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.080
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     27.530
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
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      :  0.004   0.033  12252  Z= 0.219
  Angle     :  0.808   7.888  16612  Z= 0.482
  Chirality :  0.045   0.185   1992
  Planarity :  0.007   0.057   1988
  Dihedral  : 15.151  87.752   4300
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  5.00 %
    Favored  : 94.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.82 (0.20), residues: 1476
  helix: -0.08 (0.14), residues: 1188
  sheet:  None (None), residues: 0
  loop : -2.04 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 155 
 HIS   0.004   0.001   HIS B 420 
 PHE   0.011   0.001   PHE D 450 
 TYR   0.017   0.002   TYR D 204 
 ARG   0.002   0.000   ARG B 422 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13588 (  972)
  hydrogen bonds       : angle       5.13909 ( 2892)
  covalent geometry    : bond        0.00394 (12252)
  covalent geometry    : angle       0.80812 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 406
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASN cc_start: 0.8279 (t0) cc_final: 0.7652 (t0)
REVERT: A  110 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7839 (tp30)
REVERT: A  128 TYR cc_start: 0.8299 (t80) cc_final: 0.8029 (t80)
REVERT: A  158 TRP cc_start: 0.7992 (t-100) cc_final: 0.7602 (m-10)
REVERT: A  205 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: A  214 THR cc_start: 0.8884 (p) cc_final: 0.8682 (m)
REVERT: A  419 ASP cc_start: 0.7632 (p0) cc_final: 0.7397 (p0)
REVERT: B   54 TYR cc_start: 0.8497 (t80) cc_final: 0.8273 (t80)
REVERT: B   84 ASN cc_start: 0.8203 (t0) cc_final: 0.7849 (t0)
REVERT: B  110 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7930 (tp30)
REVERT: B  128 TYR cc_start: 0.8213 (t80) cc_final: 0.7962 (t80)
REVERT: B  158 TRP cc_start: 0.8032 (t-100) cc_final: 0.7764 (m-10)
REVERT: B  198 ASN cc_start: 0.7890 (t0) cc_final: 0.7617 (t0)
REVERT: B  205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8107 (tm-30)
REVERT: B  397 GLU cc_start: 0.7850 (tp30) cc_final: 0.7641 (tp30)
REVERT: B  419 ASP cc_start: 0.7689 (p0) cc_final: 0.7422 (p0)
REVERT: C   45 GLN cc_start: 0.7268 (pm20) cc_final: 0.6914 (pm20)
REVERT: C   54 TYR cc_start: 0.8194 (t80) cc_final: 0.7895 (t80)
REVERT: C   84 ASN cc_start: 0.8204 (t0) cc_final: 0.7682 (t0)
REVERT: C  128 TYR cc_start: 0.8203 (t80) cc_final: 0.7939 (t80)
REVERT: C  158 TRP cc_start: 0.8054 (t-100) cc_final: 0.7668 (m-10)
REVERT: C  184 VAL cc_start: 0.7336 (p) cc_final: 0.6906 (p)
REVERT: C  198 ASN cc_start: 0.7887 (t0) cc_final: 0.7342 (t0)
REVERT: C  205 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7795 (tm-30)
REVERT: C  214 THR cc_start: 0.9045 (p) cc_final: 0.8786 (p)
REVERT: C  351 PHE cc_start: 0.8671 (t80) cc_final: 0.8414 (m-80)
REVERT: C  419 ASP cc_start: 0.7718 (p0) cc_final: 0.7486 (p0)
REVERT: D   84 ASN cc_start: 0.8322 (t0) cc_final: 0.7644 (t0)
REVERT: D  110 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7888 (tp30)
REVERT: D  128 TYR cc_start: 0.8325 (t80) cc_final: 0.7980 (t80)
REVERT: D  158 TRP cc_start: 0.7974 (t-100) cc_final: 0.7643 (m-10)
REVERT: D  205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7998 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 418
  average time/residue: 0.2213
  time to fit residues: 133.2127
Evaluate side-chains
  233 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 229
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  100 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 116 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 134 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 420 HIS
B 433 GLN
C  33 HIS
C 420 HIS
C 433 GLN
D 233 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.104347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.086280 restraints weight = 30290.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 4.42
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12252  Z= 0.153
  Angle     :  0.620   6.389  16612  Z= 0.324
  Chirality :  0.038   0.138   1992
  Planarity :  0.005   0.047   1988
  Dihedral  :  3.950  14.347   1628
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.85 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.72 (0.22), residues: 1476
  helix:  1.76 (0.15), residues: 1204
  sheet:  None (None), residues: 0
  loop : -1.68 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 155 
 HIS   0.005   0.001   HIS B 233 
 PHE   0.012   0.001   PHE C 450 
 TYR   0.020   0.002   TYR A 362 
 ARG   0.008   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05691 (  972)
  hydrogen bonds       : angle       3.76318 ( 2892)
  covalent geometry    : bond        0.00322 (12252)
  covalent geometry    : angle       0.62025 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 285
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASN cc_start: 0.8946 (t0) cc_final: 0.8720 (t0)
REVERT: A  110 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8392 (tp30)
REVERT: A  158 TRP cc_start: 0.8460 (t-100) cc_final: 0.7381 (m-10)
REVERT: A  197 MET cc_start: 0.5964 (tpp) cc_final: 0.5751 (tpp)
REVERT: A  205 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: A  233 HIS cc_start: 0.8861 (t-90) cc_final: 0.8473 (t70)
REVERT: A  377 MET cc_start: 0.8620 (mpp) cc_final: 0.8226 (mpp)
REVERT: A  419 ASP cc_start: 0.8783 (p0) cc_final: 0.8575 (p0)
REVERT: B   84 ASN cc_start: 0.8905 (t0) cc_final: 0.8703 (t0)
REVERT: B  110 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8428 (tp30)
REVERT: B  157 MET cc_start: 0.8528 (tpt) cc_final: 0.8281 (ttm)
REVERT: B  205 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: B  233 HIS cc_start: 0.8878 (t70) cc_final: 0.8437 (t70)
REVERT: B  379 LEU cc_start: 0.7387 (tp) cc_final: 0.7147 (tp)
REVERT: B  450 PHE cc_start: 0.8381 (t80) cc_final: 0.8133 (t80)
REVERT: C   54 TYR cc_start: 0.7832 (t80) cc_final: 0.7570 (t80)
REVERT: C   84 ASN cc_start: 0.8879 (t0) cc_final: 0.8656 (t0)
REVERT: C  128 TYR cc_start: 0.8599 (t80) cc_final: 0.8022 (t80)
REVERT: C  158 TRP cc_start: 0.8560 (t-100) cc_final: 0.7863 (m100)
REVERT: C  198 ASN cc_start: 0.7945 (t0) cc_final: 0.7579 (t0)
REVERT: C  205 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7810 (tm-30)
REVERT: C  214 THR cc_start: 0.8447 (p) cc_final: 0.8139 (t)
REVERT: C  222 MET cc_start: 0.8563 (tmm) cc_final: 0.8284 (tmm)
REVERT: C  239 MET cc_start: 0.8583 (tpp) cc_final: 0.8157 (tpp)
REVERT: C  352 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8298 (t)
REVERT: D   84 ASN cc_start: 0.8847 (t0) cc_final: 0.8556 (t0)
REVERT: D  110 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8347 (tp30)
REVERT: D  158 TRP cc_start: 0.8444 (t-100) cc_final: 0.7471 (m-10)
REVERT: D  205 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: D  214 THR cc_start: 0.8445 (m) cc_final: 0.8172 (t)
REVERT: D  377 MET cc_start: 0.8600 (mpp) cc_final: 0.8281 (mpp)
  outliers start: 33
  outliers final: 13
  residues processed: 303
  average time/residue: 0.1864
  time to fit residues: 86.5458
Evaluate side-chains
  248 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 234
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  415 VAL
Chi-restraints excluded: chain C residue  459 LEU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  415 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0020
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 117 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0670
   overall best weight:    0.5526

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 HIS
** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 407 HIS
** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.103563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.084589 restraints weight = 32055.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 4.44
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12252  Z= 0.134
  Angle     :  0.593   7.481  16612  Z= 0.303
  Chirality :  0.038   0.160   1992
  Planarity :  0.004   0.042   1988
  Dihedral  :  3.710  15.601   1624
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.13 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.52 (0.22), residues: 1476
  helix:  2.31 (0.15), residues: 1208
  sheet:  None (None), residues: 0
  loop : -1.42 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  20 
 HIS   0.003   0.001   HIS B 233 
 PHE   0.009   0.001   PHE A 450 
 TYR   0.019   0.001   TYR C 204 
 ARG   0.008   0.000   ARG D 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04938 (  972)
  hydrogen bonds       : angle       3.55081 ( 2892)
  covalent geometry    : bond        0.00280 (12252)
  covalent geometry    : angle       0.59305 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 283
  time to evaluate  : 1.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8301 (tp30)
REVERT: A  197 MET cc_start: 0.6438 (tpp) cc_final: 0.6156 (tpp)
REVERT: A  205 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: A  214 THR cc_start: 0.8421 (t) cc_final: 0.8157 (t)
REVERT: A  233 HIS cc_start: 0.8705 (t-90) cc_final: 0.8401 (t70)
REVERT: A  239 MET cc_start: 0.8754 (tpp) cc_final: 0.8424 (tpp)
REVERT: A  352 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8467 (t)
REVERT: A  377 MET cc_start: 0.8569 (mpp) cc_final: 0.8224 (mpp)
REVERT: A  379 LEU cc_start: 0.7787 (tp) cc_final: 0.7582 (tp)
REVERT: A  419 ASP cc_start: 0.8661 (p0) cc_final: 0.8436 (p0)
REVERT: B   84 ASN cc_start: 0.8886 (t0) cc_final: 0.8613 (t0)
REVERT: B  110 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8481 (tp30)
REVERT: B  141 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8343 (pttp)
REVERT: B  158 TRP cc_start: 0.8223 (t-100) cc_final: 0.7540 (m-10)
REVERT: B  197 MET cc_start: 0.6391 (tpp) cc_final: 0.6169 (tpp)
REVERT: B  205 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: B  214 THR cc_start: 0.8572 (m) cc_final: 0.8313 (t)
REVERT: B  352 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8327 (t)
REVERT: B  377 MET cc_start: 0.8884 (mmm) cc_final: 0.8403 (mpp)
REVERT: C   54 TYR cc_start: 0.8039 (t80) cc_final: 0.7814 (t80)
REVERT: C   95 SER cc_start: 0.9447 (p) cc_final: 0.9148 (p)
REVERT: C  128 TYR cc_start: 0.8809 (t80) cc_final: 0.8301 (t80)
REVERT: C  205 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: C  214 THR cc_start: 0.8611 (p) cc_final: 0.8287 (t)
REVERT: C  222 MET cc_start: 0.8696 (tmm) cc_final: 0.8408 (tmm)
REVERT: C  239 MET cc_start: 0.8875 (tpp) cc_final: 0.6862 (tpp)
REVERT: C  242 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7853 (pp20)
REVERT: C  342 TYR cc_start: 0.7308 (m-80) cc_final: 0.7010 (m-10)
REVERT: C  383 TYR cc_start: 0.8724 (t80) cc_final: 0.8336 (t80)
REVERT: D   84 ASN cc_start: 0.8796 (t0) cc_final: 0.8568 (t0)
REVERT: D  110 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8285 (tp30)
REVERT: D  157 MET cc_start: 0.8356 (tpt) cc_final: 0.8014 (ttm)
REVERT: D  158 TRP cc_start: 0.8378 (t-100) cc_final: 0.7551 (m-10)
REVERT: D  197 MET cc_start: 0.5921 (tpp) cc_final: 0.5657 (tpp)
REVERT: D  205 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: D  214 THR cc_start: 0.8607 (m) cc_final: 0.8346 (t)
REVERT: D  352 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8498 (t)
REVERT: D  377 MET cc_start: 0.8604 (mpp) cc_final: 0.8272 (mpp)
REVERT: D  379 LEU cc_start: 0.7686 (tp) cc_final: 0.7301 (tp)
  outliers start: 32
  outliers final: 18
  residues processed: 304
  average time/residue: 0.1853
  time to fit residues: 86.6251
Evaluate side-chains
  269 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 247
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  242 GLU
Chi-restraints excluded: chain C residue  415 VAL
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  459 LEU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  415 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 145 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0470
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 146 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 87 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.0682

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 HIS
C 233 HIS
D 407 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.101879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.083704 restraints weight = 31337.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 4.28
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12252  Z= 0.150
  Angle     :  0.607   9.858  16612  Z= 0.312
  Chirality :  0.039   0.168   1992
  Planarity :  0.004   0.042   1988
  Dihedral  :  3.569  15.292   1624
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.55 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.22), residues: 1476
  helix:  2.49 (0.15), residues: 1204
  sheet:  None (None), residues: 0
  loop : -1.23 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  20 
 HIS   0.005   0.001   HIS B 233 
 PHE   0.013   0.001   PHE C 183 
 TYR   0.028   0.002   TYR B  99 
 ARG   0.004   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05040 (  972)
  hydrogen bonds       : angle       3.56977 ( 2892)
  covalent geometry    : bond        0.00326 (12252)
  covalent geometry    : angle       0.60717 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 257
  time to evaluate  : 1.238 
Fit side-chains
REVERT: A  110 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8392 (tp30)
REVERT: A  130 MET cc_start: 0.9396 (mmm) cc_final: 0.8990 (mpp)
REVERT: A  205 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: A  352 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8570 (t)
REVERT: A  377 MET cc_start: 0.8640 (mpp) cc_final: 0.8319 (mpp)
REVERT: A  433 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: B   84 ASN cc_start: 0.8908 (t0) cc_final: 0.8630 (t0)
REVERT: B   95 SER cc_start: 0.9406 (p) cc_final: 0.9171 (p)
REVERT: B  110 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8546 (tp30)
REVERT: B  197 MET cc_start: 0.6400 (tpp) cc_final: 0.6138 (tpp)
REVERT: B  205 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: B  220 ASP cc_start: 0.9317 (t70) cc_final: 0.9082 (t70)
REVERT: B  377 MET cc_start: 0.8963 (mmm) cc_final: 0.8430 (mpp)
REVERT: C   54 TYR cc_start: 0.8108 (t80) cc_final: 0.7857 (t80)
REVERT: C   95 SER cc_start: 0.9431 (p) cc_final: 0.9183 (p)
REVERT: C  128 TYR cc_start: 0.8816 (t80) cc_final: 0.8375 (t80)
REVERT: C  157 MET cc_start: 0.7683 (tpt) cc_final: 0.7456 (ttp)
REVERT: C  198 ASN cc_start: 0.8356 (t0) cc_final: 0.7838 (t0)
REVERT: C  205 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7870 (tm-30)
REVERT: C  214 THR cc_start: 0.8485 (p) cc_final: 0.8164 (t)
REVERT: C  222 MET cc_start: 0.8871 (tmm) cc_final: 0.8458 (tmm)
REVERT: C  239 MET cc_start: 0.8924 (tpp) cc_final: 0.6931 (tpp)
REVERT: C  242 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7830 (pp20)
REVERT: C  342 TYR cc_start: 0.7311 (m-80) cc_final: 0.6935 (m-10)
REVERT: C  352 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8564 (t)
REVERT: C  383 TYR cc_start: 0.8694 (t80) cc_final: 0.8292 (t80)
REVERT: D   20 TRP cc_start: 0.8902 (t-100) cc_final: 0.8520 (t-100)
REVERT: D   84 ASN cc_start: 0.8922 (t0) cc_final: 0.8653 (t0)
REVERT: D  105 ASN cc_start: 0.9033 (m-40) cc_final: 0.8719 (m110)
REVERT: D  110 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8369 (tp30)
REVERT: D  157 MET cc_start: 0.8483 (tpt) cc_final: 0.8028 (ttm)
REVERT: D  197 MET cc_start: 0.6072 (tpp) cc_final: 0.5727 (tpp)
REVERT: D  205 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: D  220 ASP cc_start: 0.9272 (t70) cc_final: 0.9021 (t70)
REVERT: D  352 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8578 (t)
REVERT: D  377 MET cc_start: 0.8645 (mpp) cc_final: 0.8300 (mpp)
REVERT: D  379 LEU cc_start: 0.7700 (tp) cc_final: 0.7397 (tp)
REVERT: D  382 MET cc_start: 0.8670 (tpp) cc_final: 0.8370 (tpt)
  outliers start: 45
  outliers final: 28
  residues processed: 292
  average time/residue: 0.1826
  time to fit residues: 82.9299
Evaluate side-chains
  272 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 240
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  242 GLU
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  415 VAL
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  221 ILE
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  415 VAL
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  466 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 115 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 HIS
D  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.095672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.077823 restraints weight = 32923.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 4.26
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12252  Z= 0.245
  Angle     :  0.727  10.381  16612  Z= 0.373
  Chirality :  0.042   0.182   1992
  Planarity :  0.004   0.043   1988
  Dihedral  :  3.792  14.600   1624
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 22.31 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.22), residues: 1476
  helix:  2.34 (0.15), residues: 1204
  sheet:  None (None), residues: 0
  loop : -1.06 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  20 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.022   0.002   PHE C 183 
 TYR   0.025   0.002   TYR A  99 
 ARG   0.003   0.001   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06171 (  972)
  hydrogen bonds       : angle       3.98661 ( 2892)
  covalent geometry    : bond        0.00542 (12252)
  covalent geometry    : angle       0.72739 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 238
  time to evaluate  : 1.311 
Fit side-chains
REVERT: A  110 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8437 (tp30)
REVERT: A  141 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8441 (pttp)
REVERT: A  205 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7927 (tm-30)
REVERT: A  352 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8649 (t)
REVERT: A  377 MET cc_start: 0.8716 (mpp) cc_final: 0.8331 (mpp)
REVERT: A  426 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8768 (tp-100)
REVERT: A  433 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8603 (tm-30)
REVERT: B   84 ASN cc_start: 0.9044 (t0) cc_final: 0.8583 (t0)
REVERT: B  110 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8588 (tp30)
REVERT: B  197 MET cc_start: 0.6343 (tpp) cc_final: 0.6006 (tpp)
REVERT: B  205 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8148 (tm-30)
REVERT: B  383 TYR cc_start: 0.8418 (t80) cc_final: 0.7923 (t80)
REVERT: C   95 SER cc_start: 0.9422 (p) cc_final: 0.9133 (p)
REVERT: C  198 ASN cc_start: 0.8346 (t0) cc_final: 0.7833 (t0)
REVERT: C  205 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7624 (tm-30)
REVERT: C  214 THR cc_start: 0.8560 (p) cc_final: 0.8199 (t)
REVERT: C  222 MET cc_start: 0.8979 (tmm) cc_final: 0.8639 (tmm)
REVERT: C  342 TYR cc_start: 0.7644 (m-80) cc_final: 0.6898 (m-10)
REVERT: C  377 MET cc_start: 0.8422 (mmt) cc_final: 0.8140 (mmt)
REVERT: D   20 TRP cc_start: 0.9017 (t-100) cc_final: 0.8715 (t-100)
REVERT: D   83 LEU cc_start: 0.8956 (mm) cc_final: 0.8749 (mm)
REVERT: D  105 ASN cc_start: 0.9154 (m-40) cc_final: 0.8810 (m-40)
REVERT: D  110 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8512 (tp30)
REVERT: D  157 MET cc_start: 0.8470 (tpt) cc_final: 0.8057 (ttm)
REVERT: D  205 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8003 (tm-30)
REVERT: D  352 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8665 (t)
REVERT: D  377 MET cc_start: 0.8730 (mpp) cc_final: 0.8268 (mpp)
REVERT: D  433 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8510 (tm-30)
  outliers start: 47
  outliers final: 32
  residues processed: 277
  average time/residue: 0.1910
  time to fit residues: 83.2882
Evaluate side-chains
  251 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 217
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  459 LEU
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  466 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 121 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 130 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 129 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.098339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.080639 restraints weight = 33082.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 4.31
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12252  Z= 0.150
  Angle     :  0.656   9.957  16612  Z= 0.325
  Chirality :  0.039   0.175   1992
  Planarity :  0.004   0.043   1988
  Dihedral  :  3.594  16.705   1624
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.40 %
    Favored  : 72.16 %
  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:  2.96 (0.22), residues: 1476
  helix:  2.57 (0.15), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.96 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  20 
 HIS   0.002   0.000   HIS A  33 
 PHE   0.011   0.001   PHE D 363 
 TYR   0.024   0.002   TYR A  99 
 ARG   0.003   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05307 (  972)
  hydrogen bonds       : angle       3.63039 ( 2892)
  covalent geometry    : bond        0.00325 (12252)
  covalent geometry    : angle       0.65634 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 240
  time to evaluate  : 1.403 
Fit side-chains
REVERT: A  110 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8408 (tp30)
REVERT: A  205 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7936 (tm-30)
REVERT: A  352 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8569 (t)
REVERT: A  433 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8579 (tm-30)
REVERT: B   83 LEU cc_start: 0.9040 (mm) cc_final: 0.8828 (mm)
REVERT: B  110 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8511 (tp30)
REVERT: B  158 TRP cc_start: 0.8312 (t-100) cc_final: 0.7890 (t60)
REVERT: B  197 MET cc_start: 0.6400 (tpp) cc_final: 0.6065 (tpp)
REVERT: B  205 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: B  239 MET cc_start: 0.8755 (tpp) cc_final: 0.8414 (tpp)
REVERT: C   38 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9092 (mp)
REVERT: C   95 SER cc_start: 0.9456 (p) cc_final: 0.9209 (p)
REVERT: C  198 ASN cc_start: 0.8457 (t0) cc_final: 0.7961 (t0)
REVERT: C  205 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7796 (tm-30)
REVERT: C  214 THR cc_start: 0.8486 (p) cc_final: 0.8149 (t)
REVERT: C  222 MET cc_start: 0.8905 (tmm) cc_final: 0.8610 (tmm)
REVERT: C  352 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8599 (t)
REVERT: C  377 MET cc_start: 0.8486 (mmt) cc_final: 0.8171 (mmt)
REVERT: D   83 LEU cc_start: 0.8908 (mm) cc_final: 0.8697 (mm)
REVERT: D  105 ASN cc_start: 0.9003 (m-40) cc_final: 0.8708 (m-40)
REVERT: D  110 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8457 (tp30)
REVERT: D  157 MET cc_start: 0.8513 (tpt) cc_final: 0.8031 (ttm)
REVERT: D  158 TRP cc_start: 0.8370 (t-100) cc_final: 0.7578 (t60)
REVERT: D  197 MET cc_start: 0.6232 (tpp) cc_final: 0.6018 (tpp)
REVERT: D  205 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7441 (tm-30)
REVERT: D  239 MET cc_start: 0.8702 (tpp) cc_final: 0.8374 (tpp)
REVERT: D  352 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8620 (t)
REVERT: D  377 MET cc_start: 0.8705 (mpp) cc_final: 0.8386 (mpp)
REVERT: D  433 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8546 (tm-30)
  outliers start: 46
  outliers final: 29
  residues processed: 279
  average time/residue: 0.1814
  time to fit residues: 79.0798
Evaluate side-chains
  249 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 216
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain D residue  221 ILE
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  466 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 134 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 132 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 105 ASN
B  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.100335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.082342 restraints weight = 32392.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 4.32
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12252  Z= 0.141
  Angle     :  0.649   8.563  16612  Z= 0.323
  Chirality :  0.039   0.184   1992
  Planarity :  0.004   0.044   1988
  Dihedral  :  3.537  17.004   1624
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 24.33 %
    Favored  : 72.31 %
  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:  3.15 (0.22), residues: 1476
  helix:  2.69 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.86 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  20 
 HIS   0.002   0.000   HIS A  33 
 PHE   0.009   0.001   PHE C 346 
 TYR   0.023   0.001   TYR A  99 
 ARG   0.002   0.000   ARG D 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04990 (  972)
  hydrogen bonds       : angle       3.53728 ( 2892)
  covalent geometry    : bond        0.00302 (12252)
  covalent geometry    : angle       0.64944 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 245
  time to evaluate  : 1.280 
Fit side-chains
REVERT: A   83 LEU cc_start: 0.8734 (mm) cc_final: 0.8527 (mm)
REVERT: A   94 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8201 (mm-40)
REVERT: A   95 SER cc_start: 0.9388 (p) cc_final: 0.9025 (p)
REVERT: A  105 ASN cc_start: 0.8675 (m-40) cc_final: 0.8365 (m-40)
REVERT: A  110 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8457 (tp30)
REVERT: A  158 TRP cc_start: 0.8327 (t-100) cc_final: 0.7987 (t60)
REVERT: A  205 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7451 (tm-30)
REVERT: A  239 MET cc_start: 0.8763 (tpp) cc_final: 0.8509 (tpp)
REVERT: A  352 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8583 (t)
REVERT: A  433 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8681 (tm-30)
REVERT: B   29 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8596 (mpp80)
REVERT: B   83 LEU cc_start: 0.8984 (mm) cc_final: 0.8724 (mm)
REVERT: B   84 ASN cc_start: 0.8940 (t0) cc_final: 0.8513 (t0)
REVERT: B  110 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8805 (tp30)
REVERT: B  158 TRP cc_start: 0.8223 (t-100) cc_final: 0.7848 (t60)
REVERT: B  197 MET cc_start: 0.6460 (tpp) cc_final: 0.6142 (tpp)
REVERT: B  205 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: C   20 TRP cc_start: 0.8670 (t-100) cc_final: 0.8441 (t-100)
REVERT: C   95 SER cc_start: 0.9437 (p) cc_final: 0.9175 (p)
REVERT: C  110 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8722 (tp30)
REVERT: C  158 TRP cc_start: 0.8322 (t-100) cc_final: 0.7785 (t60)
REVERT: C  198 ASN cc_start: 0.8495 (t0) cc_final: 0.8063 (t0)
REVERT: C  205 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7282 (tm-30)
REVERT: C  214 THR cc_start: 0.8508 (p) cc_final: 0.8181 (t)
REVERT: C  222 MET cc_start: 0.8865 (tmm) cc_final: 0.8607 (tmm)
REVERT: C  352 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8726 (t)
REVERT: C  377 MET cc_start: 0.8566 (mmt) cc_final: 0.8221 (mmt)
REVERT: C  382 MET cc_start: 0.8738 (tpt) cc_final: 0.8529 (tpt)
REVERT: D   83 LEU cc_start: 0.8893 (mm) cc_final: 0.8681 (mm)
REVERT: D  105 ASN cc_start: 0.8860 (m-40) cc_final: 0.8496 (m-40)
REVERT: D  110 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8777 (tp30)
REVERT: D  158 TRP cc_start: 0.8302 (t-100) cc_final: 0.7638 (t60)
REVERT: D  160 LEU cc_start: 0.8636 (tt) cc_final: 0.8202 (mp)
REVERT: D  197 MET cc_start: 0.6375 (tpp) cc_final: 0.6155 (tpp)
REVERT: D  205 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7421 (tm-30)
REVERT: D  232 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7608 (tm-30)
REVERT: D  352 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8537 (t)
REVERT: D  377 MET cc_start: 0.8720 (mpp) cc_final: 0.8370 (mpp)
REVERT: D  426 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8711 (tp-100)
REVERT: D  433 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8618 (tm-30)
  outliers start: 45
  outliers final: 30
  residues processed: 282
  average time/residue: 0.2124
  time to fit residues: 92.0664
Evaluate side-chains
  257 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain B residue   29 ARG
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  183 PHE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  242 GLU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain C residue  459 LEU
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  221 ILE
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  466 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    0.0570
   chunk 105 optimal weight:    0.0270
   chunk 3 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 130 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.102441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.084570 restraints weight = 32187.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 4.34
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.4583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12252  Z= 0.134
  Angle     :  0.643   8.769  16612  Z= 0.317
  Chirality :  0.039   0.181   1992
  Planarity :  0.004   0.045   1988
  Dihedral  :  3.486  16.906   1624
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 25.30 %
    Favored  : 72.01 %
  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:  3.37 (0.22), residues: 1476
  helix:  2.84 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.82 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  20 
 HIS   0.002   0.000   HIS A  33 
 PHE   0.010   0.001   PHE C  63 
 TYR   0.028   0.001   TYR D  99 
 ARG   0.003   0.000   ARG B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  972)
  hydrogen bonds       : angle       3.42146 ( 2892)
  covalent geometry    : bond        0.00281 (12252)
  covalent geometry    : angle       0.64294 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 258
  time to evaluate  : 1.580 
Fit side-chains
REVERT: A   20 TRP cc_start: 0.8529 (t-100) cc_final: 0.8222 (t60)
REVERT: A   95 SER cc_start: 0.9371 (p) cc_final: 0.9034 (p)
REVERT: A  105 ASN cc_start: 0.8596 (m-40) cc_final: 0.8271 (m-40)
REVERT: A  158 TRP cc_start: 0.8272 (t-100) cc_final: 0.8004 (t60)
REVERT: A  160 LEU cc_start: 0.8589 (tt) cc_final: 0.8238 (mp)
REVERT: A  205 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7594 (tm-30)
REVERT: A  239 MET cc_start: 0.8750 (tpp) cc_final: 0.8487 (tpp)
REVERT: A  352 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8556 (t)
REVERT: A  433 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8680 (tm-30)
REVERT: B   20 TRP cc_start: 0.8542 (t-100) cc_final: 0.8272 (t60)
REVERT: B   83 LEU cc_start: 0.8835 (mm) cc_final: 0.8596 (mm)
REVERT: B   84 ASN cc_start: 0.9062 (t0) cc_final: 0.8698 (t0)
REVERT: B  160 LEU cc_start: 0.8646 (tt) cc_final: 0.8247 (mp)
REVERT: B  197 MET cc_start: 0.6448 (tpp) cc_final: 0.6148 (tpp)
REVERT: B  205 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7817 (tm-30)
REVERT: C   54 TYR cc_start: 0.8231 (t80) cc_final: 0.8020 (t80)
REVERT: C   94 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8139 (tp-100)
REVERT: C  128 TYR cc_start: 0.8922 (t80) cc_final: 0.8477 (t80)
REVERT: C  158 TRP cc_start: 0.8206 (t-100) cc_final: 0.7870 (t60)
REVERT: C  198 ASN cc_start: 0.8504 (t0) cc_final: 0.8140 (t0)
REVERT: C  205 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7503 (tm-30)
REVERT: C  214 THR cc_start: 0.8423 (p) cc_final: 0.8124 (t)
REVERT: C  222 MET cc_start: 0.8817 (tmm) cc_final: 0.8585 (tmm)
REVERT: C  239 MET cc_start: 0.8788 (tpp) cc_final: 0.6951 (tpp)
REVERT: C  242 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7579 (pp20)
REVERT: C  342 TYR cc_start: 0.7253 (m-80) cc_final: 0.6470 (m-10)
REVERT: C  377 MET cc_start: 0.8531 (mmt) cc_final: 0.8197 (mmt)
REVERT: C  380 TYR cc_start: 0.8372 (t80) cc_final: 0.8166 (t80)
REVERT: D   83 LEU cc_start: 0.8812 (mm) cc_final: 0.8564 (mm)
REVERT: D   84 ASN cc_start: 0.8950 (t0) cc_final: 0.8560 (t0)
REVERT: D  105 ASN cc_start: 0.8739 (m-40) cc_final: 0.8381 (m110)
REVERT: D  110 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8600 (tp30)
REVERT: D  158 TRP cc_start: 0.8295 (t-100) cc_final: 0.7814 (t60)
REVERT: D  160 LEU cc_start: 0.8645 (tt) cc_final: 0.8256 (mp)
REVERT: D  197 MET cc_start: 0.6345 (tpp) cc_final: 0.6131 (tpp)
REVERT: D  205 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7543 (tm-30)
REVERT: D  232 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: D  336 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8541 (pp20)
REVERT: D  352 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8660 (t)
REVERT: D  382 MET cc_start: 0.8606 (tpp) cc_final: 0.8396 (tpt)
REVERT: D  426 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8745 (tp-100)
REVERT: D  433 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8593 (tm-30)
  outliers start: 36
  outliers final: 21
  residues processed: 289
  average time/residue: 0.1852
  time to fit residues: 83.2032
Evaluate side-chains
  252 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 228
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  183 PHE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  242 GLU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  446 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 105 optimal weight:    0.5980
   chunk 35 optimal weight:    0.3980
   chunk 93 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 52 optimal weight:    0.1980
   chunk 80 optimal weight:    2.9990
   chunk 119 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9980
   chunk 139 optimal weight:    0.6980
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
B  94 GLN
C 433 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.103260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.084555 restraints weight = 32005.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 4.48
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12252  Z= 0.134
  Angle     :  0.661  11.711  16612  Z= 0.325
  Chirality :  0.039   0.173   1992
  Planarity :  0.004   0.044   1988
  Dihedral  :  3.449  16.524   1624
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 25.75 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.46 (0.22), residues: 1476
  helix:  2.91 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.79 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  20 
 HIS   0.003   0.000   HIS A  33 
 PHE   0.014   0.001   PHE D  92 
 TYR   0.030   0.002   TYR D  99 
 ARG   0.004   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04480 (  972)
  hydrogen bonds       : angle       3.39107 ( 2892)
  covalent geometry    : bond        0.00290 (12252)
  covalent geometry    : angle       0.66099 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 259
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 TRP cc_start: 0.8642 (t-100) cc_final: 0.8401 (t60)
REVERT: A  105 ASN cc_start: 0.8547 (m-40) cc_final: 0.8251 (m-40)
REVERT: A  158 TRP cc_start: 0.8345 (t-100) cc_final: 0.8049 (t60)
REVERT: A  160 LEU cc_start: 0.8638 (tt) cc_final: 0.8282 (mp)
REVERT: A  205 GLU cc_start: 0.8508 (tm-30) cc_final: 0.7547 (tm-30)
REVERT: A  239 MET cc_start: 0.8789 (tpp) cc_final: 0.8551 (tpp)
REVERT: A  433 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8693 (tm-30)
REVERT: B   20 TRP cc_start: 0.8665 (t-100) cc_final: 0.8392 (t60)
REVERT: B   83 LEU cc_start: 0.8834 (mm) cc_final: 0.8616 (mm)
REVERT: B   84 ASN cc_start: 0.9145 (t0) cc_final: 0.8776 (t0)
REVERT: B  160 LEU cc_start: 0.8607 (tt) cc_final: 0.8268 (mp)
REVERT: B  197 MET cc_start: 0.6381 (tpp) cc_final: 0.6056 (tpp)
REVERT: B  205 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8351 (tm-30)
REVERT: B  232 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: C   20 TRP cc_start: 0.8726 (t-100) cc_final: 0.8423 (t-100)
REVERT: C  158 TRP cc_start: 0.8203 (t-100) cc_final: 0.7943 (t60)
REVERT: C  198 ASN cc_start: 0.8511 (t0) cc_final: 0.8128 (t0)
REVERT: C  205 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7481 (tm-30)
REVERT: C  214 THR cc_start: 0.8423 (p) cc_final: 0.8115 (t)
REVERT: C  222 MET cc_start: 0.8848 (tmm) cc_final: 0.8628 (tmm)
REVERT: C  239 MET cc_start: 0.8797 (tpp) cc_final: 0.8500 (tpp)
REVERT: C  377 MET cc_start: 0.8530 (mmt) cc_final: 0.8261 (mmt)
REVERT: D   83 LEU cc_start: 0.8684 (mm) cc_final: 0.8484 (mm)
REVERT: D   84 ASN cc_start: 0.8998 (t0) cc_final: 0.8699 (t0)
REVERT: D   95 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9005 (p)
REVERT: D  105 ASN cc_start: 0.8708 (m-40) cc_final: 0.8345 (m110)
REVERT: D  110 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8813 (tp30)
REVERT: D  157 MET cc_start: 0.8156 (tpt) cc_final: 0.7877 (ttp)
REVERT: D  158 TRP cc_start: 0.8239 (t-100) cc_final: 0.7901 (t60)
REVERT: D  160 LEU cc_start: 0.8615 (tt) cc_final: 0.8191 (mp)
REVERT: D  197 MET cc_start: 0.6678 (tpp) cc_final: 0.6459 (tpp)
REVERT: D  205 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7567 (tm-30)
REVERT: D  232 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7733 (tm-30)
REVERT: D  336 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8579 (pp20)
REVERT: D  352 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8673 (t)
REVERT: D  382 MET cc_start: 0.8550 (tpp) cc_final: 0.8334 (tpt)
REVERT: D  426 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8747 (tp-100)
REVERT: D  433 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8598 (tm-30)
  outliers start: 41
  outliers final: 28
  residues processed: 292
  average time/residue: 0.1857
  time to fit residues: 84.1303
Evaluate side-chains
  277 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 247
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  183 PHE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  466 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 126 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 114 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 433 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.099921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.081549 restraints weight = 32189.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 4.41
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12252  Z= 0.169
  Angle     :  0.726  12.628  16612  Z= 0.361
  Chirality :  0.040   0.171   1992
  Planarity :  0.004   0.043   1988
  Dihedral  :  3.496  16.453   1624
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 26.87 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.35 (0.22), residues: 1476
  helix:  2.83 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.84 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B  20 
 HIS   0.002   0.001   HIS D 407 
 PHE   0.015   0.001   PHE C  92 
 TYR   0.032   0.002   TYR B  99 
 ARG   0.003   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05079 (  972)
  hydrogen bonds       : angle       3.55202 ( 2892)
  covalent geometry    : bond        0.00382 (12252)
  covalent geometry    : angle       0.72584 (16612)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 253
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9230 (mmm) cc_final: 0.8835 (mpp)
REVERT: A  158 TRP cc_start: 0.8450 (t-100) cc_final: 0.8101 (t60)
REVERT: A  160 LEU cc_start: 0.8593 (tt) cc_final: 0.8231 (mp)
REVERT: A  205 GLU cc_start: 0.8547 (tm-30) cc_final: 0.7675 (tm-30)
REVERT: A  214 THR cc_start: 0.8381 (t) cc_final: 0.8178 (t)
REVERT: A  433 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8677 (tm-30)
REVERT: B   83 LEU cc_start: 0.8807 (mm) cc_final: 0.8575 (mm)
REVERT: B  110 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8719 (pt0)
REVERT: B  120 GLU cc_start: 0.8189 (mp0) cc_final: 0.7986 (mp0)
REVERT: B  160 LEU cc_start: 0.8646 (tt) cc_final: 0.8260 (mp)
REVERT: B  197 MET cc_start: 0.6639 (tpp) cc_final: 0.6345 (tpp)
REVERT: B  205 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: B  232 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: C   20 TRP cc_start: 0.8892 (t-100) cc_final: 0.8594 (t-100)
REVERT: C   92 PHE cc_start: 0.8528 (m-80) cc_final: 0.8204 (m-80)
REVERT: C   95 SER cc_start: 0.9434 (p) cc_final: 0.9155 (p)
REVERT: C  110 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8843 (tp30)
REVERT: C  158 TRP cc_start: 0.8233 (t-100) cc_final: 0.7870 (t60)
REVERT: C  198 ASN cc_start: 0.8572 (t0) cc_final: 0.8136 (t0)
REVERT: C  205 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7487 (tm-30)
REVERT: C  214 THR cc_start: 0.8444 (p) cc_final: 0.8136 (t)
REVERT: C  222 MET cc_start: 0.8947 (tmm) cc_final: 0.8597 (tmm)
REVERT: C  239 MET cc_start: 0.8930 (tpp) cc_final: 0.8641 (tpp)
REVERT: C  242 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8466 (tm-30)
REVERT: C  377 MET cc_start: 0.8599 (mmt) cc_final: 0.8373 (mmt)
REVERT: D   84 ASN cc_start: 0.8969 (t0) cc_final: 0.8680 (t0)
REVERT: D   95 SER cc_start: 0.9486 (OUTLIER) cc_final: 0.9121 (p)
REVERT: D  105 ASN cc_start: 0.8868 (m-40) cc_final: 0.8490 (m-40)
REVERT: D  110 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8812 (tp30)
REVERT: D  118 GLU cc_start: 0.8880 (pm20) cc_final: 0.8647 (pm20)
REVERT: D  160 LEU cc_start: 0.8620 (tt) cc_final: 0.8236 (mp)
REVERT: D  197 MET cc_start: 0.6698 (tpp) cc_final: 0.6485 (tpp)
REVERT: D  205 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: D  232 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7841 (tm-30)
REVERT: D  382 MET cc_start: 0.8631 (tpp) cc_final: 0.8325 (tpt)
REVERT: D  433 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8556 (tm-30)
  outliers start: 34
  outliers final: 27
  residues processed: 283
  average time/residue: 0.1774
  time to fit residues: 78.3467
Evaluate side-chains
  268 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 240
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  420 HIS
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  446 VAL
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  224 CYS
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  466 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 25 optimal weight:    0.0970
   chunk 116 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 138 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 ASN
C 433 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.098297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.080074 restraints weight = 32559.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 4.39
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12252  Z= 0.191
  Angle     :  0.775  12.947  16612  Z= 0.384
  Chirality :  0.041   0.172   1992
  Planarity :  0.004   0.042   1988
  Dihedral  :  3.573  16.457   1624
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 27.01 %
    Favored  : 70.15 %
  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:  3.22 (0.22), residues: 1476
  helix:  2.75 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop : -0.88 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  20 
 HIS   0.002   0.001   HIS C  46 
 PHE   0.021   0.001   PHE C  92 
 TYR   0.033   0.002   TYR D  99 
 ARG   0.007   0.000   ARG D 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05394 (  972)
  hydrogen bonds       : angle       3.65963 ( 2892)
  covalent geometry    : bond        0.00434 (12252)
  covalent geometry    : angle       0.77506 (16612)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4320.68 seconds
wall clock time: 75 minutes 53.63 seconds (4553.63 seconds total)