Starting phenix.real_space_refine
on Fri May  9 23:42:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pke_17736/05_2025/8pke_17736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pke_17736/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pke_17736/05_2025/8pke_17736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pke_17736/05_2025/8pke_17736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pke_17736/05_2025/8pke_17736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pke_17736/05_2025/8pke_17736.cif"
  }
  resolution = 3.39
  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=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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:
    C, B, E, D, F
  Time building chain proxies: 2.08, per 1000 atoms: 0.48
  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: 0.91
  Conformation dependent library (CDL) restraints added in 476.4 milliseconds
  

  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: 0.64
  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: 1.08

  Time building geometry restraints manager: 1.08 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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:             1.160
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.830
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.090
-------------------------------------------------------------------------------
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 (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: -3.31 (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
 TRP   0.002   0.001   TRP E  79 
 HIS   0.005   0.001   HIS C  31 
 PHE   0.017   0.004   PHE A  87 
 TYR   0.010   0.002   TYR D 105 
 ARG   0.002   0.001   ARG F  21 

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

*********************** 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  : 0.424 
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: 0.1976
  time to fit residues: 33.7057
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  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   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 = 39)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.176663 restraints weight = 4880.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 2.35
r_work: 0.4242 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.4129 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.4129
-------------------------------------------------------------------------------
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 (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: -2.73 (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
 TRP   0.006   0.001   TRP C  79 
 HIS   0.001   0.000   HIS A  88 
 PHE   0.037   0.004   PHE D  64 
 TYR   0.031   0.003   TYR B 114 
 ARG   0.004   0.000   ARG C 103 

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

*********************** 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  : 0.475 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8387 (tttt) cc_final: 0.7935 (tmtt)
REVERT: A   63 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7406 (tt0)
REVERT: B   23 SER cc_start: 0.9081 (m) cc_final: 0.8857 (t)
REVERT: B   26 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8219 (mt)
REVERT: B   35 LYS cc_start: 0.8224 (tttp) cc_final: 0.7991 (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: 0.7732 (mt-10) cc_final: 0.7282 (tt0)
REVERT: D   13 MET cc_start: 0.7335 (ttm) cc_final: 0.6261 (mpp)
REVERT: D   23 SER cc_start: 0.9447 (m) cc_final: 0.8955 (m)
REVERT: D   62 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7014 (mp0)
REVERT: D   63 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6976 (tt0)
REVERT: E   13 MET cc_start: 0.7358 (ttm) cc_final: 0.6315 (mpp)
REVERT: E   23 SER cc_start: 0.9027 (m) cc_final: 0.8558 (t)
REVERT: E   63 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6944 (tt0)
REVERT: F   13 MET cc_start: 0.8144 (ttm) cc_final: 0.7192 (mtm)
  outliers start: 19
  outliers final: 12
  residues processed: 110
  average time/residue: 0.1549
  time to fit residues: 21.6106
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  : 0.426 
-------------------------------------------------------------------------------
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 33 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.6582

-------------------------------------------------------------------------------
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 = 0.4457 r_free = 0.4457 target = 0.214592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.160574 restraints weight = 5039.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 2.19
r_work: 0.4116 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.4002 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4416  Z= 0.192
  Angle     :  0.603   4.526   6006  Z= 0.341
  Chirality :  0.053   0.148    708
  Planarity :  0.004   0.025    738
  Dihedral  :  5.187  17.582    594
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 10.90 %
    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 (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: -2.50 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F  79 
 HIS   0.003   0.001   HIS A  31 
 PHE   0.017   0.003   PHE D  64 
 TYR   0.026   0.003   TYR B 114 
 ARG   0.003   0.001   ARG D 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04415 (   75)
  hydrogen bonds       : angle       5.66742 (  225)
  covalent geometry    : bond        0.00452 ( 4416)
  covalent geometry    : angle       0.60276 ( 6006)

*********************** 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
  120 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8379 (tttt) cc_final: 0.7997 (tmtt)
REVERT: A   63 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7457 (tt0)
REVERT: A   76 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8412 (mttp)
REVERT: A  116 TYR cc_start: 0.8703 (m-80) cc_final: 0.8455 (m-10)
REVERT: B  117 SER cc_start: 0.9159 (p) cc_final: 0.8744 (m)
REVERT: C   13 MET cc_start: 0.7558 (ttm) cc_final: 0.6295 (mpp)
REVERT: D   13 MET cc_start: 0.7561 (ttm) cc_final: 0.6477 (mpp)
REVERT: D   23 SER cc_start: 0.9292 (m) cc_final: 0.9017 (m)
REVERT: E   13 MET cc_start: 0.7645 (ttm) cc_final: 0.6488 (mpp)
REVERT: E   23 SER cc_start: 0.9346 (m) cc_final: 0.9086 (m)
REVERT: E   35 LYS cc_start: 0.8505 (tttt) cc_final: 0.8286 (mttt)
REVERT: E   93 VAL cc_start: 0.9195 (t) cc_final: 0.8827 (p)
REVERT: F   13 MET cc_start: 0.8332 (ttm) cc_final: 0.7273 (mtm)
REVERT: F   35 LYS cc_start: 0.8637 (tttt) cc_final: 0.8422 (mttt)
REVERT: F   92 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7092 (tm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 105
  average time/residue: 0.1186
  time to fit residues: 16.8181
Evaluate side-chains
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
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   89 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain C residue   23 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 28 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 52 optimal weight:    0.4980
   chunk 34 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4493 r_free = 0.4493 target = 0.224308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.164573 restraints weight = 4841.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.4261 rms_B_bonded: 2.19
r_work: 0.4162 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4049 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4416  Z= 0.113
  Angle     :  0.527   4.157   6006  Z= 0.298
  Chirality :  0.050   0.138    708
  Planarity :  0.004   0.026    738
  Dihedral  :  4.949  17.223    594
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.32 %
    Favored  : 82.91 %
  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: -2.34 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F  79 
 HIS   0.001   0.000   HIS A  31 
 PHE   0.029   0.002   PHE F  64 
 TYR   0.025   0.002   TYR B 114 
 ARG   0.001   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03618 (   75)
  hydrogen bonds       : angle       5.56100 (  225)
  covalent geometry    : bond        0.00271 ( 4416)
  covalent geometry    : angle       0.52651 ( 6006)

*********************** 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
  110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8394 (tttt) cc_final: 0.8047 (tmtt)
REVERT: A   63 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7571 (mt-10)
REVERT: A   76 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8360 (mttp)
REVERT: A  116 TYR cc_start: 0.8737 (m-80) cc_final: 0.8417 (m-10)
REVERT: B   76 LYS cc_start: 0.8476 (mttt) cc_final: 0.8123 (mtmm)
REVERT: B  117 SER cc_start: 0.9102 (p) cc_final: 0.8702 (m)
REVERT: C   13 MET cc_start: 0.7600 (ttm) cc_final: 0.6319 (mpp)
REVERT: C   26 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8255 (mt)
REVERT: C   34 ARG cc_start: 0.7164 (ttt-90) cc_final: 0.6651 (ttt180)
REVERT: D   13 MET cc_start: 0.7653 (ttm) cc_final: 0.6607 (mpp)
REVERT: D   23 SER cc_start: 0.9435 (m) cc_final: 0.8948 (m)
REVERT: E   13 MET cc_start: 0.7733 (ttm) cc_final: 0.6580 (mpp)
REVERT: E   23 SER cc_start: 0.9338 (m) cc_final: 0.8564 (t)
REVERT: F   13 MET cc_start: 0.8316 (ttm) cc_final: 0.7294 (mtm)
REVERT: F   64 PHE cc_start: 0.8387 (p90) cc_final: 0.8174 (p90)
  outliers start: 13
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1351
  time to fit residues: 17.7033
Evaluate side-chains
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
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   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   77 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 23 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.4402 r_free = 0.4402 target = 0.153824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.119416 restraints weight = 5010.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 2.70
r_work: 0.4040 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4416  Z= 0.152
  Angle     :  0.559   4.183   6006  Z= 0.316
  Chirality :  0.050   0.144    708
  Planarity :  0.003   0.026    738
  Dihedral  :  5.021  17.528    594
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.10 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.013   0.002   PHE F  64 
 TYR   0.024   0.002   TYR B 114 
 ARG   0.002   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03612 (   75)
  hydrogen bonds       : angle       5.46170 (  225)
  covalent geometry    : bond        0.00364 ( 4416)
  covalent geometry    : angle       0.55939 ( 6006)

*********************** 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
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8350 (tttt) cc_final: 0.7990 (tmtt)
REVERT: A   63 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7447 (mt-10)
REVERT: B   76 LYS cc_start: 0.8425 (mttt) cc_final: 0.8024 (mtmm)
REVERT: B  117 SER cc_start: 0.9125 (p) cc_final: 0.8724 (m)
REVERT: C   13 MET cc_start: 0.7431 (ttm) cc_final: 0.6128 (mpp)
REVERT: D   13 MET cc_start: 0.7450 (ttm) cc_final: 0.6350 (mpp)
REVERT: D   23 SER cc_start: 0.9379 (m) cc_final: 0.8874 (m)
REVERT: E   13 MET cc_start: 0.7583 (ttm) cc_final: 0.6394 (mpp)
REVERT: E   23 SER cc_start: 0.9270 (m) cc_final: 0.8487 (t)
REVERT: E   35 LYS cc_start: 0.8453 (tttt) cc_final: 0.8212 (mttt)
REVERT: E   93 VAL cc_start: 0.9197 (t) cc_final: 0.8779 (p)
REVERT: F   13 MET cc_start: 0.8278 (ttm) cc_final: 0.7198 (mtm)
REVERT: F   92 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6986 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 102
  average time/residue: 0.1256
  time to fit residues: 17.0395
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  : 0.447 
-------------------------------------------------------------------------------
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 A residue   93 VAL
Chi-restraints excluded: chain C residue   23 SER
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   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 46 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
F  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.148623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.115457 restraints weight = 5083.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 2.63
r_work: 0.3979 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3862 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4416  Z= 0.210
  Angle     :  0.599   4.236   6006  Z= 0.340
  Chirality :  0.052   0.148    708
  Planarity :  0.004   0.026    738
  Dihedral  :  5.278  18.409    594
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.89 %
    Favored  : 83.33 %
  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: -2.24 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  79 
 HIS   0.003   0.001   HIS B  31 
 PHE   0.016   0.002   PHE F  64 
 TYR   0.023   0.003   TYR B 114 
 ARG   0.002   0.001   ARG D 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03926 (   75)
  hydrogen bonds       : angle       5.34068 (  225)
  covalent geometry    : bond        0.00493 ( 4416)
  covalent geometry    : angle       0.59937 ( 6006)

*********************** 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
  102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7436 (ttp) cc_final: 0.7028 (ttt)
REVERT: A   35 LYS cc_start: 0.8416 (tttt) cc_final: 0.8008 (tmtt)
REVERT: A   63 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7674 (mt-10)
REVERT: B   76 LYS cc_start: 0.8597 (mttt) cc_final: 0.8254 (mtmm)
REVERT: B  117 SER cc_start: 0.9192 (p) cc_final: 0.8701 (m)
REVERT: C   13 MET cc_start: 0.7557 (ttm) cc_final: 0.6194 (mpp)
REVERT: D   13 MET cc_start: 0.7662 (ttm) cc_final: 0.6464 (mpp)
REVERT: D   23 SER cc_start: 0.9348 (m) cc_final: 0.8871 (m)
REVERT: E   13 MET cc_start: 0.7720 (ttm) cc_final: 0.6442 (mpp)
REVERT: E   23 SER cc_start: 0.9261 (m) cc_final: 0.8491 (t)
REVERT: E   93 VAL cc_start: 0.9210 (t) cc_final: 0.8763 (p)
REVERT: F   13 MET cc_start: 0.8417 (ttm) cc_final: 0.7248 (mpp)
REVERT: F   92 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7133 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1182
  time to fit residues: 15.6496
Evaluate side-chains
  99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
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 A residue   93 VAL
Chi-restraints excluded: chain C residue   23 SER
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   28 VAL
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 25 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4387 r_free = 0.4387 target = 0.153182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.119738 restraints weight = 4940.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 2.62
r_work: 0.4006 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3891 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4416  Z= 0.131
  Angle     :  0.543   4.093   6006  Z= 0.306
  Chirality :  0.050   0.143    708
  Planarity :  0.004   0.027    738
  Dihedral  :  5.119  18.600    594
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.17 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP C  79 
 HIS   0.001   0.000   HIS C  31 
 PHE   0.025   0.002   PHE E  64 
 TYR   0.023   0.002   TYR B 114 
 ARG   0.001   0.000   ARG F  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (   75)
  hydrogen bonds       : angle       5.26847 (  225)
  covalent geometry    : bond        0.00317 ( 4416)
  covalent geometry    : angle       0.54279 ( 6006)

*********************** 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
  98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8432 (tttt) cc_final: 0.8011 (tmtt)
REVERT: A   63 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7644 (mt-10)
REVERT: B   23 SER cc_start: 0.9188 (m) cc_final: 0.8771 (t)
REVERT: B   76 LYS cc_start: 0.8546 (mttt) cc_final: 0.8220 (mtmm)
REVERT: B  117 SER cc_start: 0.9146 (p) cc_final: 0.8635 (m)
REVERT: C   13 MET cc_start: 0.7511 (ttm) cc_final: 0.6226 (mpp)
REVERT: D   13 MET cc_start: 0.7635 (ttm) cc_final: 0.6466 (mpp)
REVERT: D   23 SER cc_start: 0.9358 (m) cc_final: 0.8853 (m)
REVERT: E   13 MET cc_start: 0.7710 (ttm) cc_final: 0.6435 (mpp)
REVERT: E   23 SER cc_start: 0.9234 (m) cc_final: 0.8469 (t)
REVERT: F   13 MET cc_start: 0.8457 (ttm) cc_final: 0.7261 (mpp)
REVERT: F   92 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7205 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1475
  time to fit residues: 18.2954
Evaluate side-chains
  94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
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 35 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   chunk 15 optimal weight:    9.9990
   overall best weight:    1.4182

-------------------------------------------------------------------------------
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 = 0.4373 r_free = 0.4373 target = 0.152021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.118858 restraints weight = 4965.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 2.67
r_work: 0.3997 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4416  Z= 0.154
  Angle     :  0.557   4.029   6006  Z= 0.314
  Chirality :  0.051   0.147    708
  Planarity :  0.004   0.026    738
  Dihedral  :  5.112  18.489    594
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.38 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  79 
 HIS   0.002   0.001   HIS F  31 
 PHE   0.022   0.002   PHE E  64 
 TYR   0.022   0.002   TYR E 114 
 ARG   0.001   0.000   ARG F  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (   75)
  hydrogen bonds       : angle       5.23132 (  225)
  covalent geometry    : bond        0.00370 ( 4416)
  covalent geometry    : angle       0.55732 ( 6006)

*********************** 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: 7
    poor density    : 88
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8367 (tttt) cc_final: 0.7983 (tmtt)
REVERT: A   63 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7609 (mt-10)
REVERT: B   76 LYS cc_start: 0.8385 (mttt) cc_final: 0.8071 (mtmm)
REVERT: B  117 SER cc_start: 0.9142 (p) cc_final: 0.8694 (m)
REVERT: C   13 MET cc_start: 0.7433 (ttm) cc_final: 0.6181 (mpp)
REVERT: D   13 MET cc_start: 0.7484 (ttm) cc_final: 0.6350 (mpp)
REVERT: D   23 SER cc_start: 0.9349 (m) cc_final: 0.8769 (m)
REVERT: D   34 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.6618 (ttt180)
REVERT: E   13 MET cc_start: 0.7614 (ttm) cc_final: 0.6381 (mpp)
REVERT: E   23 SER cc_start: 0.9230 (m) cc_final: 0.8468 (t)
REVERT: F   13 MET cc_start: 0.8373 (ttm) cc_final: 0.7172 (mpt)
REVERT: F   92 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7112 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1432
  time to fit residues: 17.1578
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  : 0.430 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.155722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.122593 restraints weight = 4898.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.4182 rms_B_bonded: 2.56
r_work: 0.4055 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3941 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4416  Z= 0.121
  Angle     :  0.541   4.842   6006  Z= 0.303
  Chirality :  0.050   0.142    708
  Planarity :  0.004   0.027    738
  Dihedral  :  4.946  17.925    594
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 16.03 %
    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: -2.27 (0.31), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.24), residues: 528

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03299 (   75)
  hydrogen bonds       : angle       5.23885 (  225)
  covalent geometry    : bond        0.00297 ( 4416)
  covalent geometry    : angle       0.54064 ( 6006)

*********************** 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
  90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8366 (tttt) cc_final: 0.7980 (tmtt)
REVERT: A   63 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7643 (mt-10)
REVERT: B   23 SER cc_start: 0.9105 (m) cc_final: 0.8663 (t)
REVERT: B   76 LYS cc_start: 0.8463 (mttt) cc_final: 0.8168 (mtmm)
REVERT: B  117 SER cc_start: 0.9097 (p) cc_final: 0.8665 (m)
REVERT: C   13 MET cc_start: 0.7538 (ttm) cc_final: 0.6226 (mpp)
REVERT: C   34 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6779 (tpp80)
REVERT: D   13 MET cc_start: 0.7611 (ttm) cc_final: 0.6407 (mpp)
REVERT: D   23 SER cc_start: 0.9266 (m) cc_final: 0.8728 (m)
REVERT: D   34 ARG cc_start: 0.7203 (ttt-90) cc_final: 0.6551 (ttt180)
REVERT: D   99 ASP cc_start: 0.7842 (m-30) cc_final: 0.6463 (p0)
REVERT: E   13 MET cc_start: 0.7724 (ttm) cc_final: 0.6449 (mpp)
REVERT: E   23 SER cc_start: 0.9214 (m) cc_final: 0.8448 (t)
REVERT: F   13 MET cc_start: 0.8467 (ttm) cc_final: 0.7214 (mpt)
  outliers start: 6
  outliers final: 5
  residues processed: 89
  average time/residue: 0.1543
  time to fit residues: 17.5411
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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 1 optimal weight:    0.0040
   chunk 33 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 15 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.3198

-------------------------------------------------------------------------------
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 = 0.4349 r_free = 0.4349 target = 0.149003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.116050 restraints weight = 4986.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.4110 rms_B_bonded: 2.63
r_work: 0.3959 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3845 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.5019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4416  Z= 0.229
  Angle     :  0.623   4.727   6006  Z= 0.352
  Chirality :  0.052   0.155    708
  Planarity :  0.004   0.027    738
  Dihedral  :  5.190  19.117    594
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  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 (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: -2.38 (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
 TRP   0.003   0.001   TRP C  79 
 HIS   0.003   0.001   HIS B  88 
 PHE   0.021   0.002   PHE E  64 
 TYR   0.029   0.003   TYR E 114 
 ARG   0.002   0.001   ARG C 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (   75)
  hydrogen bonds       : angle       5.25092 (  225)
  covalent geometry    : bond        0.00539 ( 4416)
  covalent geometry    : angle       0.62274 ( 6006)

********************** 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
  90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8307 (tttt) cc_final: 0.7924 (tmtt)
REVERT: A   63 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7780 (mt-10)
REVERT: B   76 LYS cc_start: 0.8591 (mttt) cc_final: 0.8231 (mtmm)
REVERT: B  117 SER cc_start: 0.9191 (p) cc_final: 0.8767 (m)
REVERT: C   13 MET cc_start: 0.7549 (ttm) cc_final: 0.6187 (mpp)
REVERT: D   13 MET cc_start: 0.7594 (ttm) cc_final: 0.6352 (mpp)
REVERT: D   23 SER cc_start: 0.9328 (m) cc_final: 0.8793 (m)
REVERT: D   34 ARG cc_start: 0.7201 (ttt-90) cc_final: 0.6611 (ttt180)
REVERT: D   78 TYR cc_start: 0.8844 (m-80) cc_final: 0.8559 (m-80)
REVERT: E   13 MET cc_start: 0.7709 (ttm) cc_final: 0.6390 (mpp)
REVERT: E   23 SER cc_start: 0.9250 (m) cc_final: 0.8496 (t)
REVERT: F   13 MET cc_start: 0.8492 (ttm) cc_final: 0.7252 (mpt)
  outliers start: 6
  outliers final: 5
  residues processed: 87
  average time/residue: 0.1513
  time to fit residues: 16.9811
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
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 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4410 r_free = 0.4410 target = 0.202622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.145025 restraints weight = 4934.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 2.58
r_work: 0.3999 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3883 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.5045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4416  Z= 0.149
  Angle     :  0.573   4.621   6006  Z= 0.322
  Chirality :  0.051   0.146    708
  Planarity :  0.004   0.028    738
  Dihedral  :  5.095  18.982    594
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.81 %
    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: -2.37 (0.30), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  79 
 HIS   0.002   0.001   HIS F  31 
 PHE   0.019   0.002   PHE E  64 
 TYR   0.026   0.002   TYR E 114 
 ARG   0.002   0.000   ARG F  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 (   75)
  hydrogen bonds       : angle       5.24154 (  225)
  covalent geometry    : bond        0.00359 ( 4416)
  covalent geometry    : angle       0.57315 ( 6006)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2501.84 seconds
wall clock time: 44 minutes 7.37 seconds (2647.37 seconds total)