Starting phenix.real_space_refine
on Fri Oct 10 11:46:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pke_17736/10_2025/8pke_17736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pke_17736/10_2025/8pke_17736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pke_17736/10_2025/8pke_17736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pke_17736/10_2025/8pke_17736.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pke_17736/10_2025/8pke_17736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pke_17736/10_2025/8pke_17736.map"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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       6      5.16       5
     C    2796      2.51       5
     N     708      2.21       5
     O     804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4314
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.89, per 1000 atoms: 0.21
  Number of scatterers: 4314
  At special positions: 0
  Unit cell: (78.09, 79.734, 45.21, 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       6     16.00
     O     804      8.00
     N     708      7.00
     C    2796      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 179.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1044

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 37.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 6.715A  pdb=" N   MET A  13 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   VAL B  16 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LYS A  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   MET B  13 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   VAL C  16 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LYS B  15 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   MET C  13 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   VAL D  16 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LYS C  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   MET D  13 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   VAL E  16 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LYS D  15 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   MET E  13 " --> pdb=" O   VAL F  14 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   VAL F  16 " --> pdb=" O   MET E  13 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LYS E  15 " --> pdb=" O   VAL F  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20
      removed outlier: 5.972A  pdb=" N   ALA A  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ALA B  19 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   ALA C  19 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ALA D  19 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   ALA E  19 " --> pdb=" O   ILE F  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26
      removed outlier: 6.409A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ALA B  25 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ALA C  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ALA D  25 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ALA E  25 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 34
    Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 62
    Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73
    Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80
      removed outlier: 6.886A  pdb=" N   SER A  77 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   TYR B  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   SER B  77 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   TYR C  78 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   SER C  77 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TYR D  78 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   SER D  77 " --> pdb=" O   LYS E  76 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TYR E  78 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   SER E  77 " --> pdb=" O   LYS F  76 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TYR F  78 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99
      removed outlier: 6.534A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL B  93 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   THR C  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   PHE B  95 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   ASN C  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ALA B  97 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL C  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   THR D  96 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   PHE C  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ASN D  98 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ALA C  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL D  93 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   THR E  96 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   PHE D  95 " --> pdb=" O   THR E  96 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ASN E  98 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ALA D  97 " --> pdb=" O   ASN E  98 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL E  93 " --> pdb=" O   VAL F  94 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   THR F  96 " --> pdb=" O   VAL E  93 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   PHE E  95 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   ASN F  98 " --> pdb=" O   PHE E  95 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ALA E  97 " --> pdb=" O   ASN F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 110
      removed outlier: 9.074A  pdb=" N   THR A 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   ALA B 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ALA A 108 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 9.074A  pdb=" N   THR B 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   ALA C 109 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA B 108 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   THR C 106 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 9.385A  pdb=" N   ALA D 109 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ALA C 108 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 9.074A  pdb=" N   THR D 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   ALA E 109 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA D 108 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   THR E 106 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   ALA F 109 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA E 108 " --> pdb=" O   ALA F 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115
    Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122

    75 hydrogen bonds defined for protein.
    225 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: 0.59

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 777
        1.32 -     1.45: 1125
        1.45 -     1.57: 2502
        1.57 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 4416
  Sorted by residual:
  bond pdb=" N   SER F  85 "
       pdb=" CA  SER F  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 9.10e-03 1.21e+04 1.41e+01
  bond pdb=" N   SER E  85 "
       pdb=" CA  SER E  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.034 9.10e-03 1.21e+04 1.36e+01
  bond pdb=" N   SER C  85 "
       pdb=" CA  SER C  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.033 9.10e-03 1.21e+04 1.30e+01
  bond pdb=" N   SER D  85 "
       pdb=" CA  SER D  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.033 9.10e-03 1.21e+04 1.30e+01
  bond pdb=" N   SER B  85 "
       pdb=" CA  SER B  85 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 9.10e-03 1.21e+04 1.26e+01
  ... (remaining 4411 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 3411
        1.29 -     2.59: 1737
        2.59 -     3.88: 694
        3.88 -     5.17: 123
        5.17 -     6.46: 41
  Bond angle restraints: 6006
  Sorted by residual:
  angle pdb=" CA  SER A  85 "
        pdb=" C   SER A  85 "
        pdb=" N   PRO A  86 "
      ideal   model   delta    sigma   weight residual
     118.16  122.33   -4.17 7.00e-01 2.04e+00 3.55e+01
  angle pdb=" CA  SER F  85 "
        pdb=" C   SER F  85 "
        pdb=" N   PRO F  86 "
      ideal   model   delta    sigma   weight residual
     118.16  122.32   -4.16 7.00e-01 2.04e+00 3.53e+01
  angle pdb=" CA  SER B  85 "
        pdb=" C   SER B  85 "
        pdb=" N   PRO B  86 "
      ideal   model   delta    sigma   weight residual
     118.16  122.29   -4.13 7.00e-01 2.04e+00 3.49e+01
  angle pdb=" CA  SER D  85 "
        pdb=" C   SER D  85 "
        pdb=" N   PRO D  86 "
      ideal   model   delta    sigma   weight residual
     118.16  122.28   -4.12 7.00e-01 2.04e+00 3.47e+01
  angle pdb=" CA  SER E  85 "
        pdb=" C   SER E  85 "
        pdb=" N   PRO E  86 "
      ideal   model   delta    sigma   weight residual
     118.16  122.26   -4.10 7.00e-01 2.04e+00 3.44e+01
  ... (remaining 6001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.54: 2223
       10.54 -    21.07: 279
       21.07 -    31.61: 48
       31.61 -    42.14: 42
       42.14 -    52.67: 12
  Dihedral angle restraints: 2604
    sinusoidal: 990
      harmonic: 1614
  Sorted by residual:
  dihedral pdb=" C   TYR E  78 "
           pdb=" N   TYR E  78 "
           pdb=" CA  TYR E  78 "
           pdb=" CB  TYR E  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.08    8.48     0      2.50e+00 1.60e-01 1.15e+01
  dihedral pdb=" C   TYR A  78 "
           pdb=" N   TYR A  78 "
           pdb=" CA  TYR A  78 "
           pdb=" CB  TYR A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.07    8.47     0      2.50e+00 1.60e-01 1.15e+01
  dihedral pdb=" C   TYR F  78 "
           pdb=" N   TYR F  78 "
           pdb=" CA  TYR F  78 "
           pdb=" CB  TYR F  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.06    8.46     0      2.50e+00 1.60e-01 1.15e+01
  ... (remaining 2601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 166
       0.058 -    0.116: 256
       0.116 -    0.174: 172
       0.174 -    0.232: 65
       0.232 -    0.290: 49
  Chirality restraints: 708
  Sorted by residual:
  chirality pdb=" CA  ILE D  20 "
            pdb=" N   ILE D  20 "
            pdb=" C   ILE D  20 "
            pdb=" CB  ILE D  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  ILE B  20 "
            pdb=" N   ILE B  20 "
            pdb=" C   ILE B  20 "
            pdb=" CB  ILE B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  ILE C  20 "
            pdb=" N   ILE C  20 "
            pdb=" C   ILE C  20 "
            pdb=" CB  ILE C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 705 not shown)

  Planarity restraints: 738
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 118 "    0.011 2.00e-02 2.50e+03   2.31e-02 5.32e+00
        pdb=" C   THR C 118 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR C 118 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR C 119 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E 118 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.28e+00
        pdb=" C   THR E 118 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR E 118 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR E 119 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 118 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.27e+00
        pdb=" C   THR A 118 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR A 118 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 119 "    0.014 2.00e-02 2.50e+03
  ... (remaining 735 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 10
        2.37 -     3.00: 2431
        3.00 -     3.63: 6016
        3.63 -     4.27: 10325
        4.27 -     4.90: 18821
  Nonbonded interactions: 37603
  Sorted by model distance:
  nonbonded pdb=" CB  PHE D  64 "
            pdb=" CZ  PHE E  64 "
     model   vdw
     1.732 3.740
  nonbonded pdb=" CB  PHE E  64 "
            pdb=" CZ  PHE F  64 "
     model   vdw
     1.733 3.740
  nonbonded pdb=" CB  PHE C  64 "
            pdb=" CZ  PHE D  64 "
     model   vdw
     1.733 3.740
  nonbonded pdb=" CB  PHE B  64 "
            pdb=" CZ  PHE C  64 "
     model   vdw
     1.733 3.740
  nonbonded pdb=" CB  PHE A  64 "
            pdb=" CZ  PHE B  64 "
     model   vdw
     1.733 3.740
  ... (remaining 37598 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.040
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.870
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.041   4416  Z= 0.962
  Angle     :  1.748   6.463   6006  Z= 1.298
  Chirality :  0.128   0.290    708
  Planarity :  0.005   0.023    738
  Dihedral  : 11.503  52.674   1560
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 0.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.31 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG F  21 
 TYR   0.010   0.002   TYR D 105 
 PHE   0.017   0.004   PHE A  87 
 TRP   0.002   0.001   TRP E  79 
 HIS   0.005   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.01262 ( 4416)
  covalent geometry    : angle       1.74779 ( 6006)
  hydrogen bonds       : bond        0.21229 (   75)
  hydrogen bonds       : angle       9.09116 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7787 (mtpp)
REVERT: A   63 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7213 (mt-10)
REVERT: A   76 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8365 (mttt)
REVERT: B   23 SER cc_start: 0.9317 (m) cc_final: 0.8796 (t)
REVERT: B   63 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7140 (mt-10)
REVERT: B  115 SER cc_start: 0.8982 (t) cc_final: 0.8760 (t)
REVERT: C   13 MET cc_start: 0.7403 (ttm) cc_final: 0.6275 (mpp)
REVERT: C   15 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7281 (mtpp)
REVERT: C   23 SER cc_start: 0.9364 (m) cc_final: 0.8841 (t)
REVERT: C   34 ARG cc_start: 0.6808 (ttt-90) cc_final: 0.6531 (ttt180)
REVERT: C   63 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7425 (mt-10)
REVERT: D   13 MET cc_start: 0.7412 (ttm) cc_final: 0.6538 (mpp)
REVERT: D   23 SER cc_start: 0.9435 (m) cc_final: 0.9177 (m)
REVERT: D   63 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6791 (mt-10)
REVERT: D  100 SER cc_start: 0.7727 (m) cc_final: 0.7495 (p)
REVERT: E   13 MET cc_start: 0.7382 (ttm) cc_final: 0.6535 (mpp)
REVERT: E   23 SER cc_start: 0.9418 (m) cc_final: 0.8883 (t)
REVERT: E   34 ARG cc_start: 0.6757 (ttt-90) cc_final: 0.6437 (ttt90)
REVERT: E   63 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6755 (mt-10)
REVERT: F   13 MET cc_start: 0.7987 (ttm) cc_final: 0.7212 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0961
  time to fit residues: 16.4919
Evaluate side-chains
  121 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.227057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.176593 restraints weight = 4949.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 2.35
r_work: 0.4247 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.4133 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4416  Z= 0.168
  Angle     :  0.662   4.839   6006  Z= 0.377
  Chirality :  0.054   0.183    708
  Planarity :  0.005   0.039    738
  Dihedral  :  4.758  16.504    594
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 11.32 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.73 (0.29), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 103 
 TYR   0.031   0.003   TYR B 114 
 PHE   0.037   0.004   PHE D  64 
 TRP   0.006   0.001   TRP C  79 
 HIS   0.001   0.000   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 4416)
  covalent geometry    : angle       0.66247 ( 6006)
  hydrogen bonds       : bond        0.05756 (   75)
  hydrogen bonds       : angle       6.20048 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8393 (tttt) cc_final: 0.7938 (tmtt)
REVERT: A   63 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7410 (tt0)
REVERT: B   23 SER cc_start: 0.9078 (m) cc_final: 0.8851 (t)
REVERT: B   26 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8216 (mt)
REVERT: B   35 LYS cc_start: 0.8226 (tttp) cc_final: 0.7993 (tttt)
REVERT: B   63 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7264 (mt-10)
REVERT: C   13 MET cc_start: 0.7349 (ttm) cc_final: 0.6054 (mpp)
REVERT: C   63 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7284 (tt0)
REVERT: D   13 MET cc_start: 0.7337 (ttm) cc_final: 0.6262 (mpp)
REVERT: D   23 SER cc_start: 0.9444 (m) cc_final: 0.8950 (m)
REVERT: D   62 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7016 (mp0)
REVERT: D   63 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6976 (tt0)
REVERT: E   13 MET cc_start: 0.7360 (ttm) cc_final: 0.6316 (mpp)
REVERT: E   23 SER cc_start: 0.9026 (m) cc_final: 0.8556 (t)
REVERT: E   63 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6943 (tt0)
REVERT: F   13 MET cc_start: 0.8142 (ttm) cc_final: 0.7190 (mtm)
  outliers start: 19
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0687
  time to fit residues: 9.7791
Evaluate side-chains
  110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain E residue   28 VAL
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    0.0770
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7142

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.227086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.171963 restraints weight = 4941.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.4303 rms_B_bonded: 2.37
r_work: 0.4205 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.4093 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4416  Z= 0.116
  Angle     :  0.542   4.266   6006  Z= 0.305
  Chirality :  0.051   0.140    708
  Planarity :  0.004   0.026    738
  Dihedral  :  4.782  15.565    594
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 12.39 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.29), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  21 
 TYR   0.024   0.002   TYR B 114 
 PHE   0.024   0.003   PHE D  64 
 TRP   0.004   0.001   TRP E  79 
 HIS   0.001   0.000   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4416)
  covalent geometry    : angle       0.54158 ( 6006)
  hydrogen bonds       : bond        0.03988 (   75)
  hydrogen bonds       : angle       5.64698 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8391 (tttt) cc_final: 0.7931 (tmtt)
REVERT: A   63 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7365 (tt0)
REVERT: A   76 LYS cc_start: 0.8603 (ptpp) cc_final: 0.8274 (mttp)
REVERT: A  116 TYR cc_start: 0.8593 (m-80) cc_final: 0.8347 (m-10)
REVERT: B   23 SER cc_start: 0.9239 (m) cc_final: 0.8721 (t)
REVERT: B   35 LYS cc_start: 0.8244 (tttp) cc_final: 0.7935 (tttt)
REVERT: B   63 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7027 (tt0)
REVERT: C   13 MET cc_start: 0.7389 (ttm) cc_final: 0.6135 (mpp)
REVERT: C   34 ARG cc_start: 0.7047 (ttt-90) cc_final: 0.6685 (ttt180)
REVERT: C   63 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7121 (tt0)
REVERT: D   13 MET cc_start: 0.7450 (ttm) cc_final: 0.6381 (mpp)
REVERT: D   23 SER cc_start: 0.9312 (m) cc_final: 0.9035 (m)
REVERT: D   63 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7077 (tt0)
REVERT: E   13 MET cc_start: 0.7493 (ttm) cc_final: 0.6394 (mpp)
REVERT: E   23 SER cc_start: 0.9296 (m) cc_final: 0.9030 (m)
REVERT: F   13 MET cc_start: 0.8184 (ttm) cc_final: 0.7164 (mtm)
  outliers start: 17
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0665
  time to fit residues: 8.8291
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   77 SER
Chi-restraints excluded: chain F residue  112 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0370
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.7864

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.212657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.158119 restraints weight = 5011.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 2.24
r_work: 0.4076 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3959 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4416  Z= 0.199
  Angle     :  0.607   4.249   6006  Z= 0.344
  Chirality :  0.052   0.144    708
  Planarity :  0.004   0.023    738
  Dihedral  :  5.187  17.856    594
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 11.75 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 103 
 TYR   0.027   0.002   TYR B 114 
 PHE   0.026   0.003   PHE F  64 
 TRP   0.005   0.001   TRP F  79 
 HIS   0.003   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 4416)
  covalent geometry    : angle       0.60727 ( 6006)
  hydrogen bonds       : bond        0.04173 (   75)
  hydrogen bonds       : angle       5.57769 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8385 (tttt) cc_final: 0.8014 (tmtt)
REVERT: A   63 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: B   76 LYS cc_start: 0.8598 (mttt) cc_final: 0.8169 (mtmm)
REVERT: B  117 SER cc_start: 0.9235 (p) cc_final: 0.8593 (m)
REVERT: C   13 MET cc_start: 0.7592 (ttm) cc_final: 0.6256 (mpp)
REVERT: D   13 MET cc_start: 0.7650 (ttm) cc_final: 0.6575 (mpp)
REVERT: D   23 SER cc_start: 0.9386 (m) cc_final: 0.8913 (m)
REVERT: E   13 MET cc_start: 0.7724 (ttm) cc_final: 0.6547 (mpp)
REVERT: E   23 SER cc_start: 0.9399 (m) cc_final: 0.8623 (t)
REVERT: E   35 LYS cc_start: 0.8376 (mttt) cc_final: 0.8127 (mtmt)
REVERT: E   93 VAL cc_start: 0.9228 (t) cc_final: 0.8858 (p)
REVERT: F   13 MET cc_start: 0.8360 (ttm) cc_final: 0.7291 (mtm)
REVERT: F   35 LYS cc_start: 0.8676 (mttt) cc_final: 0.8424 (mtpp)
REVERT: F   64 PHE cc_start: 0.8430 (p90) cc_final: 0.8200 (p90)
REVERT: F   92 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7049 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 106
  average time/residue: 0.0511
  time to fit residues: 7.4804
Evaluate side-chains
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain E residue   28 VAL
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   77 SER
Chi-restraints excluded: chain F residue  112 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0040
   chunk 26 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    3.2000

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.207234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.151059 restraints weight = 5194.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 2.14
r_work: 0.3993 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3880 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   4416  Z= 0.284
  Angle     :  0.664   4.248   6006  Z= 0.381
  Chirality :  0.054   0.157    708
  Planarity :  0.004   0.026    738
  Dihedral  :  5.636  20.569    594
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 12.82 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.32 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 103 
 TYR   0.024   0.003   TYR B 114 
 PHE   0.012   0.003   PHE E  64 
 TRP   0.004   0.001   TRP B  79 
 HIS   0.004   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 4416)
  covalent geometry    : angle       0.66402 ( 6006)
  hydrogen bonds       : bond        0.04388 (   75)
  hydrogen bonds       : angle       5.40696 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7565 (ttp) cc_final: 0.7153 (ttt)
REVERT: A   35 LYS cc_start: 0.8414 (tttt) cc_final: 0.8048 (tmtt)
REVERT: A   63 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7741 (mt-10)
REVERT: B   76 LYS cc_start: 0.8592 (mttt) cc_final: 0.8263 (mtmm)
REVERT: B  117 SER cc_start: 0.9271 (p) cc_final: 0.8696 (m)
REVERT: C   13 MET cc_start: 0.7670 (ttm) cc_final: 0.6557 (mpp)
REVERT: C   15 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7653 (mtmm)
REVERT: C  117 SER cc_start: 0.9151 (p) cc_final: 0.8907 (p)
REVERT: D   13 MET cc_start: 0.7690 (ttm) cc_final: 0.6513 (mpp)
REVERT: D   23 SER cc_start: 0.9391 (m) cc_final: 0.8945 (m)
REVERT: E   13 MET cc_start: 0.7782 (ttm) cc_final: 0.6537 (mpp)
REVERT: E   23 SER cc_start: 0.9346 (m) cc_final: 0.8624 (t)
REVERT: E   35 LYS cc_start: 0.8399 (mttt) cc_final: 0.8146 (mtmt)
REVERT: E   92 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7056 (tm-30)
REVERT: E   93 VAL cc_start: 0.9256 (t) cc_final: 0.8871 (p)
REVERT: F   13 MET cc_start: 0.8429 (ttm) cc_final: 0.7287 (mpp)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0593
  time to fit residues: 7.4449
Evaluate side-chains
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain E residue   28 VAL
Chi-restraints excluded: chain F residue  112 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.192272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.135605 restraints weight = 5194.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 2.62
r_work: 0.3922 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3811 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4416  Z= 0.269
  Angle     :  0.648   4.495   6006  Z= 0.371
  Chirality :  0.053   0.151    708
  Planarity :  0.004   0.030    738
  Dihedral  :  5.676  21.302    594
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.10 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 103 
 TYR   0.024   0.002   TYR B 114 
 PHE   0.020   0.003   PHE E  64 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.004   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 4416)
  covalent geometry    : angle       0.64822 ( 6006)
  hydrogen bonds       : bond        0.04382 (   75)
  hydrogen bonds       : angle       5.33518 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7498 (ttp) cc_final: 0.7042 (ttt)
REVERT: A   35 LYS cc_start: 0.8448 (tttt) cc_final: 0.8027 (tmtt)
REVERT: A   63 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7783 (mt-10)
REVERT: A  117 SER cc_start: 0.9115 (p) cc_final: 0.8853 (m)
REVERT: B   76 LYS cc_start: 0.8575 (mttt) cc_final: 0.8239 (mtmm)
REVERT: B   90 HIS cc_start: 0.7573 (m90) cc_final: 0.6682 (m90)
REVERT: C   13 MET cc_start: 0.7528 (ttm) cc_final: 0.6418 (mpp)
REVERT: C   15 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7544 (mtmm)
REVERT: D   13 MET cc_start: 0.7534 (ttm) cc_final: 0.6286 (mpp)
REVERT: D   23 SER cc_start: 0.9320 (m) cc_final: 0.8871 (m)
REVERT: E   13 MET cc_start: 0.7727 (ttm) cc_final: 0.6393 (mpp)
REVERT: E   23 SER cc_start: 0.9291 (m) cc_final: 0.8535 (t)
REVERT: E   34 ARG cc_start: 0.7245 (ttt-90) cc_final: 0.7042 (ttt-90)
REVERT: E   35 LYS cc_start: 0.8350 (mttt) cc_final: 0.8050 (mtmt)
REVERT: E   92 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6917 (tm-30)
REVERT: E   93 VAL cc_start: 0.9168 (t) cc_final: 0.8831 (p)
REVERT: F   13 MET cc_start: 0.8489 (ttm) cc_final: 0.7263 (mpp)
  outliers start: 11
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0604
  time to fit residues: 7.4006
Evaluate side-chains
  94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain F residue  112 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0070
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.149569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.117116 restraints weight = 5125.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 2.67
r_work: 0.3967 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.4860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4416  Z= 0.132
  Angle     :  0.561   5.045   6006  Z= 0.317
  Chirality :  0.051   0.145    708
  Planarity :  0.004   0.031    738
  Dihedral  :  5.346  20.867    594
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.81 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  21 
 TYR   0.022   0.002   TYR E 114 
 PHE   0.022   0.002   PHE E  64 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.002   0.000   HIS F  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4416)
  covalent geometry    : angle       0.56113 ( 6006)
  hydrogen bonds       : bond        0.03642 (   75)
  hydrogen bonds       : angle       5.28577 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8368 (tttt) cc_final: 0.7952 (tmtt)
REVERT: A   63 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7671 (mt-10)
REVERT: A  117 SER cc_start: 0.9034 (p) cc_final: 0.8701 (m)
REVERT: B   23 SER cc_start: 0.9228 (m) cc_final: 0.8821 (t)
REVERT: B   76 LYS cc_start: 0.8371 (mttt) cc_final: 0.8071 (mtmm)
REVERT: C   13 MET cc_start: 0.7499 (ttm) cc_final: 0.6438 (mpp)
REVERT: C   15 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7478 (mtmm)
REVERT: C   34 ARG cc_start: 0.7070 (ttt-90) cc_final: 0.6754 (tpp80)
REVERT: D   13 MET cc_start: 0.7450 (ttm) cc_final: 0.6260 (mpp)
REVERT: D   23 SER cc_start: 0.9306 (m) cc_final: 0.8769 (m)
REVERT: E   13 MET cc_start: 0.7640 (ttm) cc_final: 0.6387 (mpp)
REVERT: E   23 SER cc_start: 0.9254 (m) cc_final: 0.8505 (t)
REVERT: E   34 ARG cc_start: 0.7176 (ttt-90) cc_final: 0.6961 (ttt-90)
REVERT: E   92 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6808 (tm-30)
REVERT: F   13 MET cc_start: 0.8378 (ttm) cc_final: 0.7193 (mpt)
  outliers start: 8
  outliers final: 6
  residues processed: 92
  average time/residue: 0.0662
  time to fit residues: 7.8909
Evaluate side-chains
  91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0020
   chunk 18 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.206145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.146498 restraints weight = 4877.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 2.58
r_work: 0.4022 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3907 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4416  Z= 0.113
  Angle     :  0.538   5.619   6006  Z= 0.302
  Chirality :  0.050   0.141    708
  Planarity :  0.004   0.029    738
  Dihedral  :  5.064  19.017    594
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.88 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  21 
 TYR   0.023   0.002   TYR E 114 
 PHE   0.024   0.002   PHE E  64 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.002   0.000   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4416)
  covalent geometry    : angle       0.53818 ( 6006)
  hydrogen bonds       : bond        0.03391 (   75)
  hydrogen bonds       : angle       5.22628 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8442 (tttt) cc_final: 0.8008 (tmtt)
REVERT: A   63 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7710 (mt-10)
REVERT: B   23 SER cc_start: 0.9117 (m) cc_final: 0.8691 (t)
REVERT: C   13 MET cc_start: 0.7659 (ttm) cc_final: 0.6333 (mpp)
REVERT: C   34 ARG cc_start: 0.7244 (ttt-90) cc_final: 0.6936 (tpp80)
REVERT: D   13 MET cc_start: 0.7613 (ttm) cc_final: 0.6446 (mpp)
REVERT: D   23 SER cc_start: 0.9301 (m) cc_final: 0.8818 (m)
REVERT: E   13 MET cc_start: 0.7802 (ttm) cc_final: 0.6540 (mpp)
REVERT: E   23 SER cc_start: 0.9235 (m) cc_final: 0.8480 (t)
REVERT: F   13 MET cc_start: 0.8469 (ttm) cc_final: 0.7281 (mpt)
  outliers start: 8
  outliers final: 8
  residues processed: 92
  average time/residue: 0.0660
  time to fit residues: 7.7804
Evaluate side-chains
  90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   77 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 47 optimal weight:    0.0770
   chunk 33 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.3142

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 HIS
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.203418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.145002 restraints weight = 5057.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 2.77
r_work: 0.3993 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4416  Z= 0.151
  Angle     :  0.572   4.633   6006  Z= 0.322
  Chirality :  0.051   0.141    708
  Planarity :  0.004   0.028    738
  Dihedral  :  5.111  20.136    594
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 16.24 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 103 
 TYR   0.025   0.002   TYR E 114 
 PHE   0.025   0.002   PHE E  64 
 TRP   0.002   0.001   TRP C  79 
 HIS   0.002   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4416)
  covalent geometry    : angle       0.57245 ( 6006)
  hydrogen bonds       : bond        0.03579 (   75)
  hydrogen bonds       : angle       5.22220 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8359 (tttt) cc_final: 0.7971 (tmtt)
REVERT: A   63 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7678 (mt-10)
REVERT: B  117 SER cc_start: 0.9198 (p) cc_final: 0.8539 (m)
REVERT: C   13 MET cc_start: 0.7500 (ttm) cc_final: 0.6513 (mpp)
REVERT: C   15 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7519 (mtmm)
REVERT: C   26 ILE cc_start: 0.8394 (pt) cc_final: 0.8161 (mt)
REVERT: C   34 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6865 (tpp80)
REVERT: C   76 LYS cc_start: 0.8579 (mttp) cc_final: 0.8368 (mtmm)
REVERT: D   13 MET cc_start: 0.7460 (ttm) cc_final: 0.6301 (mpp)
REVERT: D   23 SER cc_start: 0.9306 (m) cc_final: 0.8785 (m)
REVERT: E   13 MET cc_start: 0.7679 (ttm) cc_final: 0.6427 (mpp)
REVERT: E   23 SER cc_start: 0.9244 (m) cc_final: 0.8492 (t)
REVERT: F   13 MET cc_start: 0.8390 (ttm) cc_final: 0.7228 (mpt)
  outliers start: 6
  outliers final: 5
  residues processed: 91
  average time/residue: 0.0680
  time to fit residues: 8.0044
Evaluate side-chains
  90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 46 optimal weight:    0.4980
   chunk 21 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.151178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.121154 restraints weight = 5025.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.4179 rms_B_bonded: 2.54
r_work: 0.4048 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3926 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.5129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4416  Z= 0.174
  Angle     :  0.586   4.577   6006  Z= 0.331
  Chirality :  0.051   0.140    708
  Planarity :  0.004   0.028    738
  Dihedral  :  5.167  19.594    594
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 16.45 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 103 
 TYR   0.027   0.002   TYR E 114 
 PHE   0.026   0.002   PHE E  64 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.002   0.001   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 4416)
  covalent geometry    : angle       0.58627 ( 6006)
  hydrogen bonds       : bond        0.03715 (   75)
  hydrogen bonds       : angle       5.23208 (  225)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8237 (tttt) cc_final: 0.7867 (tmtt)
REVERT: A   63 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7780 (mt-10)
REVERT: B   76 LYS cc_start: 0.8535 (mttt) cc_final: 0.8199 (mtmm)
REVERT: B  117 SER cc_start: 0.9258 (p) cc_final: 0.8705 (m)
REVERT: C   13 MET cc_start: 0.7601 (ttm) cc_final: 0.6539 (mpp)
REVERT: C   15 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7566 (mtmm)
REVERT: C   26 ILE cc_start: 0.8524 (pt) cc_final: 0.8298 (mt)
REVERT: C   34 ARG cc_start: 0.7094 (ttt-90) cc_final: 0.6792 (tpp80)
REVERT: D   13 MET cc_start: 0.7639 (ttm) cc_final: 0.6404 (mpp)
REVERT: D   23 SER cc_start: 0.9335 (m) cc_final: 0.8808 (m)
REVERT: E   13 MET cc_start: 0.7898 (ttm) cc_final: 0.6558 (mpp)
REVERT: E   23 SER cc_start: 0.9258 (m) cc_final: 0.8512 (t)
REVERT: F   13 MET cc_start: 0.8555 (ttm) cc_final: 0.7320 (mpt)
  outliers start: 5
  outliers final: 5
  residues processed: 88
  average time/residue: 0.0638
  time to fit residues: 7.2255
Evaluate side-chains
  89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain C residue   23 SER
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0040
   chunk 4 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.205946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.147211 restraints weight = 4894.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 2.64
r_work: 0.4038 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4416  Z= 0.117
  Angle     :  0.546   4.025   6006  Z= 0.307
  Chirality :  0.050   0.136    708
  Planarity :  0.004   0.028    738
  Dihedral  :  4.995  19.336    594
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 16.67 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 103 
 TYR   0.025   0.002   TYR E 114 
 PHE   0.023   0.002   PHE E  64 
 TRP   0.004   0.000   TRP D  79 
 HIS   0.002   0.000   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4416)
  covalent geometry    : angle       0.54587 ( 6006)
  hydrogen bonds       : bond        0.03369 (   75)
  hydrogen bonds       : angle       5.27698 (  225)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1227.46 seconds
wall clock time: 21 minutes 41.87 seconds (1301.87 seconds total)